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

rajat desikan rajatdesikan at gmail.com
Wed Nov 13 11:52:55 CET 2013 

An update to anyone interested:
Regenerating velocities by itself did not solve the problem. I had to
regenerate velocities and couple the upper and lower leaflets separately to
the thermostat to equilibrate the system. To smoothen the equilibration
process further, I used a 0.5 fs timestep instead of 2 fs (though this is
probably unnecessary). Thank you once more, Tsjerk.

Old .mdp:
comm-grps                = SOL DMPC
tcoupl                   = v-rescale            ; Thermostat
tc-grps                  = DMPC SOL               ; Couple lipids and SOL
separately
tau-t                    = 0.1 0.1           ; Time constant for
temperature coupling
ref-t                    = 310 310           ; Desired temperature (K)

New .mdp:
comm-grps                = SOL upper lower
tcoupl                   = v-rescale            ; Thermostat, v-rescale is
also fine
tc-grps                  = upper lower SOL             ; Couple lipid
leaflets and SOL separately
tau-t                    = 0.1 0.1 0.1             ; Time constant for
temperature coupling
ref-t                    = 310 310 310             ; Desired temperature (K)


On Wed, Nov 13, 2013 at 4:07 PM, rajat desikan <rajatdesikan at gmail.com>wrote:

> 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
>> > --
>> > gmx-users mailing list    gmx-users at gromacs.org
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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
>



-- 
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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