From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Mar 05 2018 - 02:17:25 CST
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.
Von: 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
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.
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