From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Mon Dec 27 2021 - 09:39:13 CST
Hi Ahmad,
Personally, my experience is that CHARMM-GUI is a bit conservative, especially when it comes to membranes. That being said, if you are interested in minimizing protein RMSD during the equilibration phase, you may indeed find more success extending some parts of the protocol. I’m not familiar with the exact file structure for the CHARMM-GUI outputs for NAMD (I go as far as step 5 and then do my own thing to equilibrate the systems), but you should be able to figure out what its doing based on what NAMD options are being set in the .namd file. Is it NPT? NVT? Are constraints active or extrabonds applied anywhere? A consultation with the NAMD user guide will set you straight with a bit of reading.
-Josh
From: <owner-namd-l_at_ks.uiuc.edu> on behalf of Ahmad Alqaisi <aalqais2_at_asu.edu>
Reply-To: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>, Ahmad Alqaisi <aalqais2_at_asu.edu>
Date: Sunday, December 26, 2021 at 7:49 PM
To: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
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?
Best,
Ahmad Alqaisi
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