[gmx-users] Re: Bilayer COM removal issue: Large VCM

[rajat desikan]

Hi Tsjerk,
That was very sage advice! Thank you. I will try regenerating velocities
and see if the motion goes away...


On Wed, Nov 13, 2013 at 2:00 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Rajat,
>
> If you remove comm on the bilayer, there may be relative comm between
> leaflets. If that relative motion is significant and you switch to removing
> comm per leaflet, the program suddenly finds itself resetting the com over
> a large distance. About equilibration, you equilibrated with comm_grps =
> SOL DMPC, the system is not equilibrated for another scheme. You can solve
> this issue by regenerating velocities, or by running short cycles with the
> time step increasing from very small to normal.
>
> Hope it helps,
>
> Tsjerk
>
>
> On Wed, Nov 13, 2013 at 8:06 AM, rajat desikan <rajatdesikan at gmail.com
> >wrote:
>
> > Hi All,
> > Any suggestions?
> >
> > Thanks,
> >
> >
> > On Mon, Nov 11, 2013 at 12:38 AM, rajat desikan <rajatdesikan at gmail.com
> > >wrote:
> >
> > > Hi All,
> > > I am experiencing a few problems in membrane simulations wrt COM
> removal.
> > > I downloaded a 400 ns pre-equilibrated Slipid-DMPC membrane with all
> the
> > > accompanying files. I then carried out the following steps:
> > > 1) energy minimization
> > > 2) NVT Eq - 100 ps
> > > 3) NPT Eq - 250 ps (Berendsen temp, Pres coupling)
> > >
> > > Then I used g_select to select the upper and lower DMPC leaflets. The
> > then
> > > carried out a 250 ps NPT eq again. The only change was:
> > > comm-grps                = SOL DMPC     ==>
> > > comm-grps                = SOL upper lower
> > >
> > > On every step in log file, I get the following message:
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > *        Step           Time         Lambda         124000
> > > 248.00000        0.00000 Large VCM(group lower):     -0.00051,
> > > -0.00515,     -0.00652, Temp-cm:  8.11828e+29   Energies
> > > (kJ/mol)            U-B    Proper Dih.  Improper Dih.          LJ-14
> > > Coulomb-14    7.23818e+04    4.19778e+04    6.46641e+02    4.54801e+03
> > > -1.45245e+05         LJ (SR)        LJ (LR)  Disper. corr.   Coulomb
> (SR)
> > > Coul. recip.    2.79689e+04   -3.78407e+03   -2.10679e+03
> -5.84134e+05
> > > -8.87497e+04      Potential    Kinetic En.   Total Energy
>  Temperature
> > > Pres. DC (bar)    -6.76497e+05    1.76468e+05   -5.00029e+05
> > > 3.10424e+02   -1.05704e+02 Pressure (bar)   Constr. rmsd   -1.85927e+02
> > > 6.42934e-06*
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > *Large VCM(group lower):     -0.00187,     -0.00369,      0.00032,
> > > Temp-cm:  2.02076e+29 Large VCM(group lower):     -0.00725,
> > > -0.00278,     -0.00549, Temp-cm:  1.05988e+30Large VCM(group lower):
> > > 0.00020,      0.00308,     -0.00176, Temp-cm:  1.48126e+29Large
> VCM(group
> > > lower):     -0.00541,      0.00546,     -0.00166, Temp-cm:  7.24656e+29
> > > Large VCM(group lower):     -0.00220,      0.00362,     -0.00741,
> > Temp-cm:
> > > 8.53812e+29Large VCM(group lower):      0.00140,     -0.00160,
> > > 0.00029, Temp-cm:  5.39679e+28Large VCM(group lower):     -0.00056,
> > > -0.00293,     -0.00364, Temp-cm:  2.59422e+29 Large VCM(group lower):
> > > -0.00172,     -0.00260,      0.00494, Temp-cm:  3.99945e+29Large
> > VCM(group
> > > lower):      0.00252,      0.00594,      0.00068, Temp-cm:
>  4.93342e+29*
> > > *DD  step 124999  vol min/aver 0.702  load imb.: force  1.3%  pme
> > > mesh/force 0.636*
> > >
> > > I do not know what to make of it. There are no issues when I remove COM
> > > for the entire system. I have seen this issue come up a few times in
> the
> > > archives too, but I didn't find a satisfactory solution since the
> bilayer
> > > was very well equilibrated.
> > >
> > > I would appreciate any suggestions. Thank you.
> > >
> > >
> > > --
> > > Rajat Desikan (Ph.D Scholar)
> > > Prof. K. Ganapathy Ayappa's Lab (no 13),
> > > Dept. of Chemical Engineering,
> > > Indian Institute of Science, Bangalore
> > >
> >
> >
> >
> > --
> > Rajat Desikan (Ph.D Scholar)
> > Prof. K. Ganapathy Ayappa's Lab (no 13),
> > Dept. of Chemical Engineering,
> > Indian Institute of Science, Bangalore
> > --
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
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-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore