[gmx-users] Re: Unsteady Density

Peter C. Lai pcl at uab.edu
Tue May 24 21:40:15 CEST 2011

Fabian Casteblanco <fabian.casteblanco at gmail.com> wrote:

>Thanks Justin.
>I'm currently running the MD run separately so that the average value
>won't be affected by the unequilibrated values at the beginning of the
>NPT run where the density started in the 400s and ran up to the ~high
>700s.  I had done this before when I had nstlist at 5 but I did run
>NPT for a lot shorter time last time so Im hoping this time it will be
>better since last time it was still off (0.781 g/cm3 to 0.791 g.cm3).
>I will also change the compressibility.  Do you think increasing the
>rlist, rcoulomb, rvdw value to about 1.6, 1.8 nm might also work a bit
I would not play with those too much, since CHARMM users typically do not publish with those cutoffs. You may want look at going from vdwtype cutoff to vdwtype switch and start the vdwswitch at 0.8, however.

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