Recent changes to QuickStartGuide-NAMD

QuickStartGuide-NAMD modified by Shun Sakuraba

Shun Sakuraba — Thu, 11 Apr 2024 07:11:45 -0000

--- v43
+++ v44
@@ -1,13 +1,15 @@
 Quick Start Guide: NAMD (for ver. 0.2.x and ver. 0.3.x)
 ====
+
+## Important note for users
+**Currently there are no CHARMM / NAMD users in dev team, and script for CHARMM/NAMD is currently not very well maintained. If you found any strange / suspicious behavior please let us know!**

 Preparing topology
 ----

 Download CHARMM force field parameters from http://mackerell.umaryland.edu/CHARMM_ff_params.html, and copy both CHARMM22 force field file (top_all22_prot.inp) and stream parameters for ETOH (stream/toppar_all22_prot_model.str) to working directory. Run VMD (http://www.ks.uiuc.edu/Research/vmd/), and type the following into VMD’s Tk console (accessible via Extensions -> Tk console).

-~~~~
-::::tcl
+~~~~tcl
 topology top_all22_prot.inp
 topology toppar_all22_prot_model.str
 resetpsf

QuickStartGuide-NAMD modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Mon, 06 May 2019 14:20:29 -0000

--- v42
+++ v43
@@ -64,13 +64,11 @@
 Inside these directories, `soln/MDinfo`, `soln/MolPrm1`, `soln/SltInfo`, `refs/MDinfo`, `refs/MolPrm1`, and `refs/SltInfo` files are generated.
 See [Parameter files for ermod](parameters-ermod03) for detailed description of SltInfo, MolPrm1, and so on.

-Caution:
-When the number of solute molecules in the solution system of interest is more than unity, user needs to modify MDinfo, MolPrmX, and SltInfo manually.
+**Caution**:  When the number of solute molecules in the solution system of interest is more than unity, user needs to modify MDinfo, MolPrmX, and SltInfo manually.
 See [Finite concentration of solute: when more than one molecules are present for the solute species](MoreThanOneSolute).
-The manual modification of MDinfo, MolPrmX, and SltInfo in the case of more than one solute molecules is necessary only for NAMD.
+The manual modification of MDinfo, MolPrmX, and SltInfo in the case of more than one solute molecules is necessary only for NAMD (and CHARMM).

-Caution:
-When ERmod is of ver 0.3.5 or earlier, the solution MD needs to be arranged so that the solute molecule appears as the first molecule in the coordinate files. This restriction is true only in the case of NAMD. Further, even when the solution MD is not arranged so, one can run ermod correctly if MDinfo, MolPrmX, and SltInfo are modified by hand. Still, this modification needs the knowledge about the structure of the input files for ermod, it is advised that the solute molecule be placed as the first in the coordinate files when the solution MD is conducted with NAMD. Note that the above restriction is removed as of ver 0.3.6.
+**Caution**:  When ERmod is of ver 0.3.5 or earlier, the solution MD needs to be arranged so that the solute molecule appears as the first molecule in the coordinate files. This restriction is true only in the case of NAMD (and CHARMM). Further, even when the solution MD is not arranged so, one can run ermod correctly when MDinfo, MolPrmX, and SltInfo are modified manually. Still, this modification needs the knowledge about the structure of the input files for ermod, it is advised that the solute molecule be placed as the first in the coordinate files when the solution MD is conducted with NAMD (or CHARMM). Note that the above restriction is removed as of ver 0.3.6.

 soln/MDinfo should read as

QuickStartGuide-NAMD modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Mon, 06 May 2019 07:58:12 -0000

--- v41
+++ v42
@@ -65,7 +65,7 @@
 See [Parameter files for ermod](parameters-ermod03) for detailed description of SltInfo, MolPrm1, and so on.

 Caution:
-When the number of solute molecules in the solution system of interest is more than unity, user needs to modify MDinfo, MolPrmX, and SltInfo.
+When the number of solute molecules in the solution system of interest is more than unity, user needs to modify MDinfo, MolPrmX, and SltInfo manually.
 See [Finite concentration of solute: when more than one molecules are present for the solute species](MoreThanOneSolute).
 The manual modification of MDinfo, MolPrmX, and SltInfo in the case of more than one solute molecules is necessary only for NAMD.

QuickStartGuide-NAMD modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Mon, 06 May 2019 07:57:27 -0000

--- v40
+++ v41
@@ -66,7 +66,7 @@

 Caution:
 When the number of solute molecules in the solution system of interest is more than unity, user needs to modify MDinfo, MolPrmX, and SltInfo.
-See
+See [Finite concentration of solute: when more than one molecules are present for the solute species](MoreThanOneSolute).
 The manual modification of MDinfo, MolPrmX, and SltInfo in the case of more than one solute molecules is necessary only for NAMD.

 Caution:

QuickStartGuide-NAMD modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Mon, 06 May 2019 07:56:42 -0000

--- v39
+++ v40
@@ -64,7 +64,13 @@
 Inside these directories, `soln/MDinfo`, `soln/MolPrm1`, `soln/SltInfo`, `refs/MDinfo`, `refs/MolPrm1`, and `refs/SltInfo` files are generated.
 See [Parameter files for ermod](parameters-ermod03) for detailed description of SltInfo, MolPrm1, and so on.

-Note that the solution MD needs to be arranged so that the solute molecule appears as the first molecule in the coordinate files. This restriction is true only in the case of NAMD. Further, even when the solution MD is not arranged so, one can run ermod correctly if MDinfo, MolPrmX, and SltInfo are modified by hand. Still, this modification needs the knowledge about the structure of the input files for ermod, it is advised that the solute molecule be placed as the first in the coordinate files when the solution MD is conducted with NAMD.
+Caution:
+When the number of solute molecules in the solution system of interest is more than unity, user needs to modify MDinfo, MolPrmX, and SltInfo.
+See
+The manual modification of MDinfo, MolPrmX, and SltInfo in the case of more than one solute molecules is necessary only for NAMD.
+
+Caution:
+When ERmod is of ver 0.3.5 or earlier, the solution MD needs to be arranged so that the solute molecule appears as the first molecule in the coordinate files. This restriction is true only in the case of NAMD. Further, even when the solution MD is not arranged so, one can run ermod correctly if MDinfo, MolPrmX, and SltInfo are modified by hand. Still, this modification needs the knowledge about the structure of the input files for ermod, it is advised that the solute molecule be placed as the first in the coordinate files when the solution MD is conducted with NAMD. Note that the above restriction is removed as of ver 0.3.6.

 soln/MDinfo should read as

QuickStartGuide-NAMD modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Tue, 30 Oct 2018 08:37:11 -0000

--- v38
+++ v39
@@ -108,7 +108,7 @@
 ~~~~

 If the program runs successfully, there should be files named engsln.xx and aveuv.tt, where xx is a two-digit integer, besides several other outputs.
-The former is the histogram of the solute-solvent pair interaction energy, while the latter is the histogram of solute self energy.
+The former is the histogram of the solute-solvent pair interaction energy, while the latter is the averaged sum of the solute-solvent interaction energy.
 The two-digit numbers indicate which fraction of the trajectory the file corresponds to.
 For example, the trajectory is divided into 10 blocks.
 engsln.01 is then the histogram obtained from the first one of the 10 blocks, and engsln.02 is from the second one of the 10 blocks.

QuickStartGuide-NAMD modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Tue, 30 Oct 2018 08:34:46 -0000

--- v37
+++ v38
@@ -107,7 +107,7 @@
 (ERmod directory)/bin/ermod
 ~~~~

-If the program runs successfully, there should be files named engsln.xx and slfeng.xx, where xx is a two-digit integer, besides several other outputs.
+If the program runs successfully, there should be files named engsln.xx and aveuv.tt, where xx is a two-digit integer, besides several other outputs.
 The former is the histogram of the solute-solvent pair interaction energy, while the latter is the histogram of solute self energy.
 The two-digit numbers indicate which fraction of the trajectory the file corresponds to.
 For example, the trajectory is divided into 10 blocks.

QuickStartGuide-NAMD modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Tue, 26 Jun 2018 05:23:44 -0000

--- v36
+++ v37
@@ -62,7 +62,7 @@
 In the example case, the ethanol molecule is the solute; type “ETOH” (do not include quotation marks) to proceed.
 After the execution, two directories are created, namely soln and refs.
 Inside these directories, `soln/MDinfo`, `soln/MolPrm1`, `soln/SltInfo`, `refs/MDinfo`, `refs/MolPrm1`, and `refs/SltInfo` files are generated.
-See [Parameter files for ermod (ver 0.2)](parameters-ermod02) or [Parameter files for ermod (ver 0.3)](parameters-ermod03) for detailed description of SltInfo, MolPrm1, and so on.
+See [Parameter files for ermod](parameters-ermod03) for detailed description of SltInfo, MolPrm1, and so on.

 Note that the solution MD needs to be arranged so that the solute molecule appears as the first molecule in the coordinate files. This restriction is true only in the case of NAMD. Further, even when the solution MD is not arranged so, one can run ermod correctly if MDinfo, MolPrmX, and SltInfo are modified by hand. Still, this modification needs the knowledge about the structure of the input files for ermod, it is advised that the solute molecule be placed as the first in the coordinate files when the solution MD is conducted with NAMD.

@@ -83,7 +83,7 @@
 But the number of molecular species in refs/MDinfo is 1, since MDinfo in this case carries the information of the pure solvent system.

 Both in the soln and refs directories, MolPrm1 and SltInfo should be found.
-MolPrm1 is the parameter file for solvent molecule, and SltInfo is the parameter file for solute. Both files contain the Lennard-Jones parameters and charge information, which are necessary in the calculation. See [Parameter files for ermod (ver 0.2)](parameters-ermod02) or [Parameter files for ermod (ver 0.3)](parameters-ermod03) for detailed description of MDInfo, SltInfo, MolPrm1, and so on.
+MolPrm1 is the parameter file for solvent molecule, and SltInfo is the parameter file for solute. Both files contain the Lennard-Jones parameters and charge information, which are necessary in the calculation. See [Parameter files for ermod](parameters-ermod03) for detailed description of MDInfo, SltInfo, MolPrm1, and so on.

 Now the parameters for the solution system are prepared.
 Move to soln directory and run the helper script:
@@ -142,7 +142,7 @@
 The trajectory is divided into a set of blocks both for soln and refs.
 The default value of the number of divisions is 10 for the solution system and is 5 for the reference.
 The number of divisions can be modified with the numdiv parameter in the parameters_er file when the ermod program is run.
-See [Parameter files for ermod (ver 0.2)](parameters-ermod02) or [Parameter files for ermod (ver 0.3)](parameters-ermod03) for the description of the parameters which can be specified in parameters_er.
+See[Parameter files for ermod](parameters-ermod03) for the description of the parameters which can be specified in parameters_er.

 If the solute is rigid (its intramolecular structure is fixed), the procedure is simplified.
 The scheme for the solution part is the same as above.
@@ -162,5 +162,5 @@
 The third argument, --rigid, specifies that the test-particle insertion calculation is performed with fixed structure of the solute.
 The option --rigid can be simplified to -r.
 The structure of the solute is taken from the SltInfo file when the solute is rigid.
-See [Parameter files for ermod (ver 0.2)](parameters-ermod02) or [Parameter files for ermod (ver 0.3)](parameters-ermod03) for the format of the SltInfo file in the case of rigid solute.
+See [Parameter files for ermod](parameters-ermod03) for the format of the SltInfo file in the case of rigid solute.
 When the refs calculation is done, the calculation of solvation free energy of rigid solute can be done with the same procedure as that in the flexible case.

QuickStartGuide-NAMD modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Tue, 30 Aug 2016 05:15:36 -0000

--- v35
+++ v36
@@ -55,7 +55,7 @@
 (ERmod directory)/share/ermod/tools/NAMD/gen_structure --psf solution.psf --log solution_run.log
 ~~~~

-where (ERmod directory) is the directory where the ERmod programs are installed; the directory was specified with the option of --prefix of ./configure described in [build-Guide].
+where (ERmod directory) is the directory where the ERmod programs are installed; the directory was specified with the option of --prefix of ./configure described in [General build guide](build-Guide).
 The log file specified as the last argument can be any log file that uses solution.psf (is only used to find appropriate parameter files).
 The options --psf and --log can be simplified to -t and -l, respectively. 
 path/to/ermod should be replaced with an appropriate path from the current working directory. Upon execution, user specifies the solute segment name.

QuickStartGuide-NAMD modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 09 Jan 2015 07:23:59 -0000

--- v34
+++ v35
@@ -48,7 +48,7 @@
 Generate input configuration for solvation free energy calculation
 ----

-Input configuration files for ermod and slvfe will be generated via a few helper scripts. First, execute the following command to generate an input file containing the system information:
+Input configuration files for ermod and slvfe will be generated via a few helper scripts. First, execute the following command to generate an input file containing the system information:

 ~~~~
 ::::sh
@@ -64,7 +64,7 @@
 Inside these directories, `soln/MDinfo`, `soln/MolPrm1`, `soln/SltInfo`, `refs/MDinfo`, `refs/MolPrm1`, and `refs/SltInfo` files are generated.
 See [Parameter files for ermod (ver 0.2)](parameters-ermod02) or [Parameter files for ermod (ver 0.3)](parameters-ermod03) for detailed description of SltInfo, MolPrm1, and so on.

-Note that the solution MD needs to be arranged so that the solute molecule appears as the first molecule in the coordinate files. This restriction is true only in the case of NAMD. Further, even when the solution MD is not arranged so, one can run ERmod correctly if MDinfo, MolPrmX, and SltInfo are modified by hand. Still, this modification needs the knowledge about the structure of the input files for ermod, it is advised that the solute molecule be placed as the first in the coordinate files when the solution MD is conducted with NAMD.
+Note that the solution MD needs to be arranged so that the solute molecule appears as the first molecule in the coordinate files. This restriction is true only in the case of NAMD. Further, even when the solution MD is not arranged so, one can run ermod correctly if MDinfo, MolPrmX, and SltInfo are modified by hand. Still, this modification needs the knowledge about the structure of the input files for ermod, it is advised that the solute molecule be placed as the first in the coordinate files when the solution MD is conducted with NAMD.

 soln/MDinfo should read as