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

[rajat desikan]

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        0.00000Large 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+29Large 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+29Large 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+29Large 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