From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Mar 06 2018 - 01:50:42 CST
You can just add a line:
margin 3
to the namd input file. This will mostly prevent namd from aborting on large box shrink on the cost of performance. Therefore, after the 1st initial shrink, you can restart the npt without margin since the box won’t shrink that much again. Actually the reason why it shrinks so much initially, is that the solvation tool you used (but almost all do) gave the system a too small density.
Norman
Von: Ashutosh Shandilya [mailto:scfbioiitd_at_gmail.com]
Gesendet: Montag, 5. März 2018 22:04
An: Norman Geist <norman.geist_at_uni-greifswald.de>
Betreff: Re: namd-l: periodic cell has become too small for original patch grid
Thanks for your help. I switched off the Langevin piston (nvt.namd) and it ran fine but now when I am switching to npt stepwise it has again the same error. I am restarting with old coordinate, vel, xsc but still, the problem persists. Could you explain how to you margin or any other modification in the input file? I want to run a targeted MD and production input file is also attached.
Attached are my input files. Kindly have a look and suggest.
Many thanks,
Ash
On Mon, Mar 5, 2018 at 3:17 AM, Norman Geist <norman.geist_at_uni-greifswald.de <mailto:norman.geist_at_uni-greifswald.de> > wrote:
Altough you called it nvt.namd, ist actually npt since it includes constant pressure control (langevinpiston). It is therefore expected that the cell volume shrinks. Sometimes, depending on the initial conditions, the box shrinks so much, that box decomposition due parallelization becomes ineffective and namd aborts. Solutions are:
1. Just restart from coor,vel,xsc if already there
2. (Easier but slower) Use “margin“ in your script set to e.g. 2-5 Angstrom.
Gl
Norman
Von: owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu> [mailto:owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu> ] Im Auftrag von Ashutosh Shandilya
Gesendet: Freitag, 2. März 2018 20:55
An: namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>
Betreff: namd-l: periodic cell has become too small for original patch grid
Dear NAMD users
I came across a most common error but could not find solution online. I have a system and I am trying to run TMD. After minimization, during heating I am getting this error. I have tried to modify my input files several times but still I get error after 3400 steps. I also tried to restart this after different checkpoints but still this problem persists. Could you suggest any modification in my input files to run this system smoothly. I visualized the minimization trajectory, nothing looked abnormal to me. Attached are my stepwise minimization and heating input files. Kindly suggest.
Ash
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