From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Feb 08 2019 - 02:59:55 CST
Just my cents, I’m using a 4fs timestep without any problems (even REMD) by applying the hydrogen mass repartitioning scheme. As I’m using the amber forcefield, this modification can simnply be applied on the parm7 topology file using ParmED.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Denish Poudyal
Gesendet: Freitag, 8. Februar 2019 02:46
An: David Hardy <dhardy_at_ks.uiuc.edu>
Cc: NAMD list <namd-l_at_ks.uiuc.edu>
Betreff: Re: namd-l: MSM grid values
Yes, the grid spacing remains 2.5 A, however for the MSMminx/MSMmaxx and corresponding values along y and z can vary. And in many cases, I got the error saying some atoms are out of the grid and I have been trying to adjust the MSMmin/max values. Worst thing is this error pops out after few hours of simulation.
On Fri, Feb 8, 2019 at 2:28 AM David Hardy <dhardy_at_ks.uiuc.edu <mailto:dhardy_at_ks.uiuc.edu> > wrote:
Generally, the grid spacing should be on the order of 2 to 3 Angstroms for a 12 A cutoff.
NAMD will make good choices for MSM by default, assuming you are simulating atoms.
-- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy_at_ks.uiuc.edu <mailto:dhardy_at_ks.uiuc.edu> , http://www.ks.uiuc.edu/~dhardy/ On Feb 6, 2019, at 11:15 PM, Denish Poudyal <qrystal45_at_gmail.com <mailto:qrystal45_at_gmail.com> > wrote: How do we assign the MSMx/y/z values in a simulation? Denish Poudyal CDPTU, Nepal -- Denish Poudyal CDPTU, Nepal
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