[gmx-users] NVT to NPT. Works on a single processor, does VT to NPT. Works on a single processor, does not work on 4 ????

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sat Oct 27 19:15:57 CEST 2007

>> > Hi
>> >
>> > I seem to be doing something wrong here, but cannot figure out what.
>> >
>> > -  I have run a 200 ps NVT simulation for a lipid bilayer on 4
>> > processors using the gromacs-3.3.1 build.
>> >
>> > - The last frame from the NVT simulation was used in conjunction with
>> > a newly written .mdp file to restart the simulation using grompp.
>> > (Before doing this, the trajectory and the final .gro file were
>> > deshuffled).
>> >
>> > - When the NPT .tpr is built for 4 processors (using -shuffle and
>> > -sort), the NPT simulation immediately explodes perhaps because the
>> > density is high (1100 kg/m3). However, if the NPT .tpr is built for a
>> > single cpu, then the simulation does not immediately explode, and has
>> > run now for at least 3000 steps. (the .edr file from NVT was not
>> > used). The same mdp file was used to generate both the 4-cpu tpr and
>> > the 1-cpu tpr.
>> >
>> > Why should this happen ??? I am hoping I have made some mistake here.

Could also be the use of -sort. As a test, try not using it while  
still using -shuffle in a NP=4 simulation.

When you grompp with -t .trr and -sort in combination then it expects  
the .trr file to be pre-sorted. It makes no sense to require a  
pre-sorted file prior to the sorting method. This is (I think) the  
reason why gromacs doesn't fully support the -sort option. If you want  
to use the -sort option then download g_desort from the user  
contributions and go through the documentation very carefully. It's  
complicated because of the need to have a pre-sorted .trr file.

Probably you could just not use a .trr file at all... I don't think  
that that would invalidate your ensemble as long as you are not  
restarting ridiculously often.

So the bottom line answer to your question is that your .trr that you  
are loading in is not pre-sorted and so the order of atoms is  
incorrect and bonded atoms are found to be very far apart. Hence the  
huge forces and then the explosion.

Hope it helps,

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