[gmx-users] Membrane simulation npt problem

[VITALY V. CHABAN]

it is short, but this is not the reason for crash.

this sort of problems come from topology.





On Sat, Jan 16, 2016 at 6:15 AM, Marco Franzoi <marco.franzoi89 at gmail.com>
wrote:

> Thanks vitaly. Can it be that the nvt equilibration is too short for such
> a huge system?
> Il 16/gen/2016 03:42, "VITALY V. CHABAN" <vvchaban at gmail.com> ha scritto:
>
>> The problem is outside your parameter file.
>>
>>
>>
>>
>>
>> On Fri, Jan 15, 2016 at 3:56 PM, Marco Franzoi <marco.franzoi89 at gmail.com
>> >
>> wrote:
>>
>> > Good evening to everyone.
>> >
>> > I've an issue regarding a membrane simulation.
>> > I've downloaded an already equilibrated POPE/POPG membrane and, to test
>> the
>> > system, I run an em, a 0.1 ns nvt and 1 ns npt simulation and everything
>> > was fine.
>> >
>> > Then, I've raised the cell lenght in the z direction and added a
>> peptide,
>> > solvate, ionized and minimized. The next ntv step was also fine but,
>> when I
>> > run the npt simulation, suddenly the cell broadens in xy directions and
>> > shrinks in z direction.
>> >
>> > What can be wrong with it?
>> >
>> > My npt.mpd file is attached.
>> >
>> > Thanks for your help!
>> >
>> > Marco FRANZOI
>> > PhD Student
>> > University of Padua
>> > Department of biology, V floor South
>> > Tel: 3405086908
>> > Mail: marco.franzoi89 at gmail.com
>> >
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>