Re: gamd restart file in namd 2.13

From: Aravinda Munasinghe (aravinda1879_at_gmail.com)
Date: Wed Dec 04 2019 - 10:54:20 CST

Dear Andrew,
Thank you very much for your reply. It seems to work as it should be.
Thank you,
Best,

Aravinda Munasinghe
PhD Candidate |*|* Colina Research Group
https://colina.chem.ufl.edu/
George and Josephine Butler Polymer Research Laboratory
Center for Macromolecular Science and Engineering
Department of Chemistry |*|* University of Florida
Vice President of Mayors' Council
http://mayorscouncil.housing.ufl.edu/

On Wed, Dec 4, 2019 at 10:55 AM Pang, Yui Tik <andrewpang_at_gatech.edu> wrote:

> Hi Aravinda,
>
> I am sorry the website was a bit confusing but no you do not need to set
> accelMDGRestartFile when accelMDGRestart is off. The GaMD restart file is
> indeed created following the general procedures of writing restart files
> and read in when accelMDGRestartFile is set and accelMDGRestart is on.
>
> Best,
> Andrew (Yui Tik Pang)
> ------------------------------
> *From:* owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of
> Aravinda Munasinghe <aravinda1879_at_gmail.com>
> *Sent:* Tuesday, December 3, 2019 9:17 AM
> *To:* namd-l_at_ks.uiuc.edu <namd-l_at_ks.uiuc.edu>
> *Subject:* namd-l: gamd restart file in namd 2.13
>
> Dear All,
> I am trying to run gamd within namd 2.13. I have been using keywords in
> http://miao.compbio.ku.edu/GaMD/tutorial_namd.html to define associated
> parameters needed for NAMD gamd setup. So, when I run the conventional MD
> and GaMD equilibration step, I have the following parameters within the
> namd section.
> accelMD on
> accelMDdual on
> accelMDdihe on
> accelMDG on
> accelMDGiE 1
> accelMDGRestart off
> accelMDGcMDSteps 3000000
> accelMDGEquiSteps 20000000
> accelMDGcMDPrepSteps 200000
> accelMDGEquiPrepSteps 200000
> accelMDOutFreq 5000
> accelMDGsigma0P 6.0
> accelMDGsigma0D 6.0
> accelMDGRestartFile pDMAEMA75_syn_opt3_out.restart.gamd
>
> I was under the impression that when "accelMDGRestart off" is set,
> NAMD uses the file name at
> "accelMDGRestartFile pDMAEMA75_syn_opt3_out.restart.gamd" to create restart
> files. However, NAMD never creates the file named
> "pDMAEMA75_syn_opt3_out.restart.gamd", but it do create a restart file
> appending $outputname.restart.gamd
> my question is when namd restart files are created, does NAMD follow the
> general procedure of writing restart files and append the ".restart.gamd"
> for gamd related restart file?. And when we want to continue the
> simulation, the corresponding restart file will be read into (in my case
> "pDMAEMA75_syn_opt3_out.restart.gamd") through "accelMDGRestartFile"
> keyword?.
>
> I was a little confused about why,
> accelMDGRestartFile pDMAEMA75_syn_opt3_out.restart.gamd
> needed to be defined at step one since it does not require any gamd
> restart file.
> Thank you,
> Best,
> Aravinda Munasinghe
> --
> Aravinda Munasinghe,
>
>

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