Fw: Re: [gmx-users] Methanol SOL :Number of solventmolecules = 0

[sharada]

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 ..
Started Steepest Descents on node 0 Tue Dec 11 17:48:57 2007
Removing pbc first time
Done rmpbc
Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+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
              0        0.00000        0.00000
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 at gromacs.org)
-------------------------------------------------------
Now where do I go from here? Its asking me to energy minimize the system which 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.
regards
sharada
 
-- Original Message --
From: "Xavier Periole" <X.Periole at rug.nl>
To: Discussion list for GROMACS users <gmx-users at 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 :
SOL    XXX
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  <sharada at ccmb.res.in> wrote:
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> 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
> [asd at ccmb 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
>        -nice    int      0  Set the nicelevel
>       -[no]v   bool    yes  Be loud and noisy
>        -time   real     -1  Take frame at or first after this time.
>          -np    int      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 for 1 node...
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7#
> checking input for internal consistency...
> calling /lib/cpp...
> processing topology...
> Generated 141 of the 1176 non-bonded parameter combinations
> Excluding 3 bonded neighbours for Protein 1
> Cleaning up temporary file grompp5RBSRX
> -------------------------------------------------------
> Program grompp, VERSION 3.3
> Source code file: toppush.c, line: 1264
>Fatal error:
> No such moleculetype SOL
> -------------------------------------------------------
> I never prefer working in root as I know  the problems. Thanks for 
> suggesting. I needed to change the methanol.itp and methanol216.gro which 
>could be possible only through root. 
> regards
> sharada 
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-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
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