Re: [GaMD-discuss] Restarting GAMD

[Miao, Y. <Yin...@me...>]

Hi Hazrati,

I’m CC’ing Keya, an expert in GaMD in the lab, and she may help with your questions.

Best,
Yinglong


Yinglong Miao, Ph.D.
Associate Professor
Department of Pharmacology and
Computational Medicine Program
University of North Carolina - Chapel Hill
Tel: 1-919-962-5696
http://miaolab.org

Editor-in-Chief
npj Drug Discovery
https://www.nature.com/npjdrugdiscov

On Oct 21, 2025, at 7:00 AM, Mehrnoosh Khodam Hazrati via GaMD-discuss <gam...@li...> wrote:

Dear GAMD experts,

I was running a GAMD simulation for 2 microseconds in AMBER22, but the run crashed. Now, with irest = 1, and irest_gamd = 1, and using the following command, I'm trying to restart my job:
pmemd.cuda -i job4.in -o gamd4.out -p input.prmtop -c gamd3.ncrst -ref gamd3.ncrst -r gamd4.ncrst -x gamd4.nc -gamd gamd4.log
My first question is if I'm doing it correctly. And my second question is how to merge gamd3.log and gamd4.log to get the total log file. As I noticed, the gamd4.log starts again from the initial time (same as gamd3.log).

I appreciate any help.

Best regards,
Hazrati _______________________________________________
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