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

[rajat desikan]

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:
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> *        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*
>
>
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> *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