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<DIV><FONT face=Arial size=2>I’m running MD of lipid membrane made of three
types of lipids (PS, PC, PE)<BR>I always get VCM after about 300 to 400
ps. <BR>In my *.mdp file I’m using to groups lipidpcpeps and sol_ion for
<BR>center of mass motion removal and temperature coupling. <BR>I tried
using different configurations for my groups then <BR>position restraints
lipids but I didn’t<BR>help. What can I do to solve this
problem?</FONT></DIV>
<DIV> </DIV><FONT face=Arial size=2>
<DIV><BR>---------------------------------------------------------------------------------------<BR>Error
message in log file:</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>
Step
Time
Lambda<BR>
90000
180.00002 0.00000</DIV>
<DIV> </DIV>
<DIV> Rel. Constraint Deviation: Max between
atoms RMS<BR> Before
LINCS 0.048160
4236 4238
0.018847<BR> After
LINCS 0.000018
5223 5224 0.000004</DIV>
<DIV> </DIV>
<DIV> Energies
(kJ/mol)<BR>
Bond
Angle Proper Dih. Ryckaert-Bell. Improper
Dih.<BR> 1.09413e+04
1.60613e+04 5.94364e+03
3.61899e+03
8.39084e+02<BR>
LJ-14
Coulomb-14 LJ (SR) Coulomb
(SR) Coulomb (LR)<BR> 9.19145e+03
-5.51505e+04 3.34016e+04 -4.03104e+05
-1.55198e+05<BR> Position Rest.
Potential Kinetic En. Total
Energy Temperature<BR>
3.18901e+04 -5.01565e+05 9.08787e+04
-4.10686e+05 3.00361e+02<BR> Pressure
(bar)<BR> -5.80396e+02<BR>Large VCM(group lipidpcpeps):
12860086.00000, 5915031552.00000, 60308048.00000, ekin-cm:
1.84720e+24</DIV>
<DIV> </DIV>
<DIV>-----------------------------------------------------------------------------------------<BR>my
mdp file:</DIV>
<DIV> </DIV>
<DIV><BR>title
= blona 4ns ps pe
pc<BR>cpp
=
/lib/cpp<BR>define
=
-DFLEX_SPC<BR>constraints
=
hbonds<BR>integrator
=
md<BR>dt
= 0.002 ; ps
!<BR>nsteps
= 1000000
<BR>nstxout
=
20000<BR>nstvout
=
20000<BR>nstfout
=
20000<BR>nstlog
=
10000<BR>nstenergy
=
10000<BR>nstxtcout
=
10000<BR>nstlist
=
10<BR>ns_type
=
grid<BR>rlist
= 0.9</DIV>
<DIV> </DIV>
<DIV>; Method for doing
VdW<BR>vdw-type
=
Cut-off<BR>rvdw
= 0.9</DIV>
<DIV> </DIV>
<DIV>; Method for doing
electrostatics<BR>coulombtype
=
PME<BR>rcoulomb
= 0.9<BR>fourierspacing =
0.12<BR>fourier_nx =
0<BR>fourier_ny =
0<BR>fourier_nz =
0<BR>pme_order
= 4<BR>ewald_rtol
= 1e-5<BR>optimize_fft =
yes</DIV>
<DIV> </DIV>
<DIV><BR>; Berendsen temperature coupling is on in two
groups<BR>Tcoupl
=
berendsen<BR>tc-grps
= sol_ion lipidpcpeps
<BR>tau_t
= 0.01
0.01<BR>ref_t
= 300 300 <BR>; Energy
monitoring<BR>energygrps =
PC PE PS SOL Na</DIV>
<DIV> </DIV>
<DIV>; Generate velocites is off at 300
K.<BR>;gen_vel
=
yes<BR>gen_temp
=
300.0<BR>;gen_seed
= 173529<BR>; Groups for center of mass motion
removal<BR>comm-grps
= sol_ion lipidpcpeps<BR>; Mode for center of mass motion
removal<BR>comm-mode
= linear<BR>; Center of mass
control<BR>nstcomm
= 1</DIV>
<DIV> </DIV>
<DIV>; Periodic boundary
conditions<BR>pbc
= xyz</DIV>
<DIV> </DIV>
<DIV>----------------------------------------------------------------------------<BR></FONT></DIV></BODY></HTML>