Dear Dr. Xavier Periole,
Thank you for guiding me through. I could solve the problem of setting up the
system for minimization. However When started minimization run for 2000 steps
with steepest descent , I encountered yet another problem. which is as follows
..
Methanol optimization:
Started Steepest Descents on node 0 Tue Dec 11 17:48:57 2007
Removing pbc first time
Done rmpbc
Steepest Descents:
Tolerance (Fmax) = 1.0e+01
Number of steps= 2000
Grid: 4 x 5 x 4 cells
calc_bor: cg0=0, cg1=553, ncg=553
CG0[0]=0, CG1[0]=553
CG0[1]=0, CG1[1]=0
calc_bor: cg0=0, cg1=553, ncg=553
CG0[0]=0, CG1[0]=553
CG0[1]=0, CG1[1]=0
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.
Step Time Lambda
00.00.0
calc_bor: cg0=0, cg1=553, ncg=553
CG0[0]=0, CG1[0]=553
CG0[1]=0, CG1[1]=0
Program mdrun, VERSION 3.3
Source code file: nsgrid.c, line: 226
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been within [ 0 .. 80 ]
Please report this to the mailing list (gmx-users@gromacs.org)
Now where do I go from here? Its asking me to energy minimize the system which
is what I am trying to do ! What is this ci value and why is it so high? Kindly
help me I am once again stuck. Furthermore, when I minimized the same peptide
in SPC216 water box of 1108 water molecules for 2000 steps this error did not
appear. When I compared the md.log files in both the cases I found that in case
of water optimization of SPC water was enabled where as this line for methanol
was missing which should mean that the energies are shooting off scale is
that right ? Should I optimize my system in vacuo before simmulating in
methanol?
Water optimization:
{Generated table with 500 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Enabling SPC water optimization for 1108 molecules.
Initiating Steepest Descents
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest, initial mass: 3396
Started Steepest Descents on node 0 Wed Dec 12 15:52:11 2007
Removing pbc first time
Done rmpbc
Steepest Descents:
Tolerance (Fmax) = 1.0e+01
Number of steps= 2000
Going to use C-settle (1108 waters)
wo = 0.33, wh =0.33, wohh = 3, rc = 0.08165, ra = 0.0384897
rb = 0.0192449, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1
Grid: 4 x 5 x 4 cells}
regards
sharada
-- Original Message --
From: Xavier Periole [EMAIL PROTECTED]
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Tue, 11 Dec 2007 12:07:27 +0100
Subject: Re: Fw: Re: [gmx-users] Methanol SOL :Number of solvent molecules
= 0
in your agg2t.top you should replace the last line :
SOLXXX
by:
Methanol XXX
which is the name of the molecule.
You should also remove the angle definition in methanol.itp. Placing
a ; at the beginning of the line is enough.
XAvier
On Tue, 11 Dec 2007 15:40:04 +0530 (IST)
sharada [EMAIL PROTECTED] wrote:
Dear Mark Abraham,
I have changed MeoH to SOL in .gro and .itp files and also changed the
#include line to methanol.itp
It now seemed to have written the solvent molecules in the top file with SOL
as the name with atom types of methanol.
When I ran grompp program as following I get the error as shown below: I am
also attaching the .gro,.itp,.top files. for information. Did I miss out
anything ?
grompp -f em.mdp -c agg2_b4em.gro -p agg2.top -o agg2_em.tpr
[EMAIL PROTECTED] Aggregates]$ grompp -f em.mdp -c agg2_b4em.gro -p agg2.top
-o
agg2_em.tpr
Option Type Value Description
--
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-niceint 0 Set the nicelevel
-[no]v boolyes Be loud and noisy
-time real -1 Take frame at or first after this time.
-npint 1 Generate statusfile for # nodes
-[no]shuffle bool no Shuffle molecules over nodes
-[no]sort bool no Sort molecules according to X coordinate
creating statusfile
