[gmx-users] Re: parallel job crash for large system

2011-08-22 Thread Dr. Vitaly V. Chaban
>> Does a different barostat work? No. Switching to Berendsen barostat did not help. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.o

Re: [gmx-users] Re: parallel job crash for large system

2011-08-22 Thread Mark Abraham
On 23/08/2011 10:49 AM, Dr. Vitaly V. Chaban wrote: On 23/08/2011 8:44 AM, Dr. Vitaly V. Chaban wrote: In the below issue, the barostat is setup semiisotropically and works only along the "long" direction. The density of the system slowly grows due to mixing. If this can be useful Does a di

[gmx-users] Re: parallel job crash for large system

2011-08-22 Thread Dr. Vitaly V. Chaban
On Mon, Aug 22, 2011 at 9:02 PM, Dr. Vitaly V. Chaban wrote: >> Your density seems to be about 70% of what I would expect. Are you >> sure that this is not just a normal case of a poorly equilibrated >> system crashing? That matches with what you say about the density >> growing (although perhaps

[gmx-users] Re: parallel job crash for large system

2011-08-22 Thread Dr. Vitaly V. Chaban
> Your density seems to be about 70% of what I would expect. Are you > sure that this is not just a normal case of a poorly equilibrated > system crashing? That matches with what you say about the density > growing (although perhaps it has more to do with poor equilibration > than with mixing, as y

[gmx-users] Re: parallel job crash for large system

2011-08-22 Thread Dr. Vitaly V. Chaban
> > On 23/08/2011 8:44 AM, Dr. Vitaly V. Chaban wrote: >> In the below issue, the barostat is setup semiisotropically and works >> only along the "long" direction. The density of the system slowly >> grows due to mixing. If this can be useful > > Does a different barostat work? No idea. Shou

[gmx-users] Re: parallel job crash for large system

2011-08-22 Thread chris . neale
Your density seems to be about 70% of what I would expect. Are you sure that this is not just a normal case of a poorly equilibrated system crashing? That matches with what you say about the density growing (although perhaps it has more to do with poor equilibration than with mixing, as you

Re: [gmx-users] Re: parallel job crash for large system

2011-08-22 Thread Mark Abraham
On 23/08/2011 8:44 AM, Dr. Vitaly V. Chaban wrote: In the below issue, the barostat is setup semiisotropically and works only along the "long" direction. The density of the system slowly grows due to mixing. If this can be useful Does a different barostat work? Mark On Mon, Aug 22, 201

[gmx-users] Re: parallel job crash for large system

2011-08-22 Thread Dr. Vitaly V. Chaban
In the below issue, the barostat is setup semiisotropically and works only along the "long" direction. The density of the system slowly grows due to mixing. If this can be useful On Mon, Aug 22, 2011 at 5:32 PM, Dr. Vitaly V. Chaban wrote: > We are running the system consisting of 84000 atom