Re: namd-l digest V1 #3189

From: Raman Preet Singh (
Date: Mon Dec 27 2021 - 07:08:59 CST

Hello Ahmad,

It is unclear what do you mean by simulation stability. CHARMM-GUI produces fairly nice inputs but, of course, you may need to modify the input files based on your requirements, especially the number of steps. One important aspect to understand is that even if you use the same input files and run it three times, the results will vary. This is because of the rounding-off of the decimal places and the systems could diverge right from the first step. So, a short run (say, 5 ns) will show differences in RMSD values.

It would be a better idea to contact CHARMM-GUI team, they have a very short turnaround time for any issues.


From: namd-l digest <>
Sent: Monday, December 27, 2021, 1:30 PM
Subject: namd-l digest V1 #3189

namd-l digest Monday, December 27 2021 Volume 01 : Number 3189

In this issue:

    namd-l: Question about CHARMM-GUI NAMD Inputs


Date: Mon, 27 Dec 2021 02:41:30 +0200
From: Ahmad Alqaisi <>
Subject: namd-l: Question about CHARMM-GUI NAMD Inputs

Hello all,

I have been using the CHARMM-GUI server to generate NAMD input files for MD
simulations. I noticed that inputs from this server give bad results in
many cases, especially in terms of RMSD values and simulation stability.

Can you give any suggestion on how to improve the inputs generated by
CHARMM-GUI to get better results? For example, the equilibration time in
the CHARMM-GUi protocol is much smaller than other protocols like QwikMD.
If I increase the equilibration time, would that give me better results?

Also, can anyone give a description of the protocol that is carried in the
CHARMM-GUI input files ? For example the file named
step4_equilibration.inp, does it contain minimization, annealing and
equilibration or only minimization and equilibration?

Ahmad Alqaisi


End of namd-l digest V1 #3189

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