[gmx-users] Re: NPT for compressing

[Vitaly Chaban]

Incredible!


On Mon, May 23, 2011 at 11:40 AM, Elisabeth <katesedate at gmail.com> wrote:
> Thanks for your hint. Employing a 0.5 fs timestep resolved the problem.
>
> On 20 May 2011 22:58, Vitaly Chaban <vvchaban at gmail.com> wrote:
>>
>> > 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