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

[Tsjerk Wassenaar]

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
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Tsjerk A. Wassenaar, Ph.D.