[gmx-users] dppc's simulation

[Chen Hao]

Dear David:
It seems you are right. But now I have another question, first I simulate at constant volume(NVT) to equilibrate, everything is ok, then when I do simulation at constant pressure(NPT), mdrun report the following messages and freeze:

Step 8  Warning: pressure scaling more than 1%, mu: 1.01356 1.01356 1.01356

Step 10  Warning: pressure scaling more than 1%, mu: 0.913651 0.913651 0.913651

Step 11  Warning: pressure scaling more than 1%, mu: 1.14953 1.14953 1.14953

Step 12  Warning: pressure scaling more than 1%, mu: 1.37388 1.37388 1.37388

Step 13  Warning: pressure scaling more than 1%, mu: 0.536957 0.536957 0.536957
Warning: 1-4 interaction at distance larger than 1
These are ignored for the rest of the simulation
turn on -debug for more information
Wrote pdb files with previous and current coordinates

Step 14  Warning: pressure scaling more than 1%, mu: 465.889 465.889 465.889

Back Off! I just backed up step14.pdb to ./#step14.pdb.1#
Wrote pdb files with previous and current coordinates
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
         Box (3x3):
            Box[    0]={        NaNQ,         NaNQ,         NaNQ}
            Box[    1]={        NaNQ,         NaNQ,         NaNQ}
            Box[    2]={        NaNQ,         NaNQ,         NaNQ}
         Can not fix pbc.

Back Off! I just backed up step15.pdb to ./#step15.pdb.1#
Wrote pdb files with previous and current coordinates
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
         Box (3x3):
            Box[    0]={        NaNQ,         NaNQ,         NaNQ}
            Box[    1]={        NaNQ,         NaNQ,         NaNQ}
            Box[    2]={        NaNQ,         NaNQ,         NaNQ}
         Can not fix pbc.

Back Off! I just backed up step16.pdb to ./#step16.pdb.1#
Wrote pdb files with previous and current coordinates
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
         Box (3x3):
            Box[    0]={        NaNQ,         NaNQ,         NaNQ}
            Box[    1]={        NaNQ,         NaNQ,         NaNQ}
            Box[    2]={        NaNQ,         NaNQ,         NaNQ}
         Can not fix pbc.

Back Off! I just backed up step17.pdb to ./#step17.pdb.1#
Wrote pdb files with previous and current coordinates
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
         Box (3x3):
            Box[    0]={        NaNQ,         NaNQ,         NaNQ}
            Box[    1]={        NaNQ,         NaNQ,         NaNQ}
            Box[    2]={        NaNQ,         NaNQ,         NaNQ}
         Can not fix pbc.

Back Off! I just backed up step18.pdb to ./#step18.pdb.1#
Wrote pdb files with previous and current coordinates
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
         Box (3x3):
            Box[    0]={        NaNQ,         NaNQ,         NaNQ}
            Box[    1]={        NaNQ,         NaNQ,         NaNQ}
            Box[    2]={        NaNQ,         NaNQ,         NaNQ}
         Can not fix pbc.
Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 210]

What's the matter?

My grompp.mdp file:
title                    = dppc
cpp                      = /lib/cpp
integrator               = md
nsteps                   = 10000
nstlist                  = 10
nstxout                  = 100
nstvout                  = 0
nstxtcout                = 0
nstlog                   = 100
dt                       = 0.001
nstenergy                = 100
ns_type                  = grid
coulombtype              = cut-off
rlist                    = 1.2
rvdw                     = 1.2
rcoulomb                 = 1.8
tcoupl                   = berendsen
tc_grps                  = dppc sol
tau_t                    = 0.01 0.01
ref_t                    = 323 323
Pcoupl                   = berendsen
pcoupltype               = isotropic
tau_p                    = 0.05
ref_p                    = 1.0
compressibility          = 4.5e-5
constraints              = all-bonds
constraint-algorithm     = shake
 
----- Original Message ----- 
From: "David" <spoel at xray.bmc.uu.se>
To: <gmx-users at gromacs.org>
Sent: Friday, February 21, 2003 1:54 PM
Subject: Re: [gmx-users] dppc's simulation


> On Fri, 2003-02-21 at 06:05, kzong wrote:
> > Dear all:
> > I want to do some simulation about dppc bilayer, but I have some trouble. Because I build the initial structure with charmm, firstly I modify atom name according to the definition in dppc.itp(download from Dr.Tieleman's website) and convert pdb file to gro file by pdb2gmx, then I modify the example2.top(also from Dr.Tieleman's website) to fit my own system and write my own grompp.mdp file based the same file in gromacs benchmark package. When I run grompp and mdrun program, everything seems ok. But when I check the output coordinate file, I found that it's very different from the initial coordinate file even since only after 1 step. It seems that the coordinate file and topology file isn't consistent. But what's the matter? Have anything addition need to pay attention to?
> > 
> <
> things may look very different when in fact it is only periodic boundary
> conditions in action.(i.e. lipids moving ot the other side of the box)
> 
> 
> -- 
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, Dept. of Cell and Molecular Biology
> Husargatan 3, Box 596,  75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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