Rahul Godawat wrote:
Here are the details of my .mdp file, I use PME, cutoff 1.0 nm, and time
step 2 fs...... and OS --- RedHat Enterprise Linux, I hv been using 3.2.1
for a while apart from that no specific reason for using 3.2.1
dt = 0.002 ; time step (ps)
nsteps = 100000 ; number of steps
comm_mode = Linear
comm_grps = System
energygrps = OW HW
try removing the line above
nstcomm = 10 ; reset c.o.m. motion
nstxout = 500 ; write coords
nstvout = 500 ; write velocities
nstlog = 500 ; print to logfile
nstenergy = 500 ; print energies
nstlist = 10 ; update pairlist
ns_type = grid ; pairlist method
coulombtype = PME
rvdw = 1.0 ; cut-off for vdw
rcoulomb = 1.0 ; cut-off for coulomb
rlist = 1.0 ; cut-off for coulomb
Tcoupl = Berendsen
tc-grps = System
tau_t = 0.5
ref_t = 300
Thanks
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Today's Topics:
1. Free volume: Pass and Gromacs (Alessandro Mattozzi)
2. Re: Free volume: Pass and Gromacs (David van der Spoel)
3. Re: Freezing part of the molecules!!! (Soren Enemark)
4. Re: Freezing part of the molecules!!! (David van der Spoel)
5. shake vs settle for water (Rahul Godawat)
6. diffusivity computations (Debashis Dutta)
7. Re: shake vs settle for water (David van der Spoel)
----------------------------------------------------------------------
Message: 1
Date: Wed, 7 Jun 2006 17:11:03 +0200
From: "Alessandro Mattozzi" <[EMAIL PROTECTED]>
Subject: [gmx-users] Free volume: Pass and Gromacs
To: <gmx-users@gromacs.org>
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Hi all
I wonder if anybody has been using Pass to measure free volume: I got these
errors:
-Error: Found an odd element (B) on atom #13454. Hydrogen radius assigned.
Suggestion: Do I have to remove all the dummies?
-Segmentation fault
Suggestion: I use trjconv to get a pdb; is it possible that I am doing some
mistake in the conversion?
Thanx
Alessandro Mattozzi
M.Phil., Ph.D. student
Dept. of Fibre and Polymer Technology
Royal Institute of Technology
Stockholm, Sweden
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Message: 2
Date: Wed, 07 Jun 2006 17:14:59 +0200
From: David van der Spoel <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Free volume: Pass and Gromacs
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
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Alessandro Mattozzi wrote:
Hi all
I wonder if anybody has been using Pass to measure free volume: I got
these errors:
-Error: Found an odd element (B) on atom #13454. Hydrogen radius
assigned.
Suggestion: Do I have to remove all the dummies?
Yes.
make an index file, it will have a suitable group for it.
-Segmentation fault
Suggestion: I use trjconv to get a pdb; is it possible that I am doing
some mistake in the conversion?
Thanx
Alessandro Mattozzi
M.Phil., Ph.D. student
Dept. of Fibre and Polymer Technology
Royal Institute of Technology
Stockholm, Sweden
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________________________________________________________________________
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