[gmx-users] Re: NPT for compressing

Vitaly Chaban vvchaban at gmail.com
Sat May 21 07:58:42 CEST 2011

> When I use constraints for all-bonds and dt of 0.002 compressing the box
> works well and I get density of above 600 SI which is the actual density of
> alkane. Can any one help why setting no constraints and dt=0.001 leads to
> the error message shown above. When no constraints is used PR doesnt work
> for compressing and berendsen gives desired densty only for high pressures
> above 50 bar. I need to study my system at different pressures from 10
> bar... please comment on this.. Thanks.

Use smaller time-step while you are compressing the system. This
should eliminate the above problems.

Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216

More information about the gromacs.org_gmx-users mailing list