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

sharada sharada at ccmb.res.in
Wed Dec 12 13:04:36 CET 2007 


    
        
            

            
                
                    
                        
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)   =  1.00000e+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 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)   =  1.00000e+01
   Number of steps    =         2000
Going to use C-settle (1108 waters)
wo = 0.333333, wh =0.333333, 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" <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:
> 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 
-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
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