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Dear users<BR>
I was tyring to run an npt simulation of membrane. My mdp is:<BR>
<BR><FONT size=2>
constraints = all-bonds<BR>
integrator = md<BR>
dt = 0.002 ; ps !<BR>
nsteps = 50000 ; total 100 ps.<BR>
nstcomm = 1<BR>
nstxout = 250<BR>
nstenergy = 100<BR>
nstlist = 10<BR>
ns_type = grid<BR>
pbc = xyz<BR>
coulombtype = PME<BR>
vdwtype = cut-off<BR>
; Berendsen temperature coupling is on in two groups<BR>
; aniisotropic pressure coupling is now on<BR>
Tcoupl = berendsen<BR>
Pcoupl = Parrinello-Rahman<BR>
pcoupltype = semiisotropic<BR>
tc-grps = POPC SOL<BR>
tau_t = 0.1 0.1<BR>
ref_t = 300 300<BR>
ref_p = 1 1<BR>
tau_p = 10<BR>
compressibility = 4.5e-5 4.5e-5<BR>
; Energy monitoring<BR>
energygrps = POPC SOL<BR>
; Generate velocites is off at 300 K.<BR>
gen_vel = yes<BR>
gen_temp = 300.0<BR>
gen_seed = 173529<BR>
comm_grps = POPC SOL<BR></FONT>
<BR>
As advised in a recent workshop on <A href="http://www.csc.fi/chem/course/gmx2007/">http://www.csc.fi/chem/course/gmx2007/</A> i am using Parrinello-Rahman instead of berendsen. The problem is that the box size is getting reduced to <FONT size=2>9.99448 9.99448 9.25077 from 10.0 10.0 10.0 and water is compressing the bilayer.</FONT><BR>
<FONT size=2>I also tried anisotropic coupling</FONT><BR><FONT size=2><FONT size=2>
pcoupltype = anisotropic<BR>
tc-grps = POPC SOL<BR>
tau_t = 0.1 0.1<BR>
ref_t = 300 300<BR>
ref_p = 1 1 1 0 0 0<BR>
tau_p = 10<BR>
compressibility = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0<BR>
This time my box size is reducing to <FONT size=2>9.99065 9.99717 9.17646.</FONT><BR>
<FONT size=2>I cant figure out the problem. Any help will be appreciated.<BR></FONT></FONT></FONT><br /><hr />Fly HYD-BLR for Rs.499 Log on to MakeMyTrip! <a href='http://ss1.richmedia.in/recurl.asp?pid=266' target='_new'>Check it out!</a></body>
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