[gmx-users] NVT

[Junfang.Zhang at csiro.au]

Hi David,

Thank you so much for the prompt reply.

When I use genbox to insert 1 methane, it seems ok, but if 4 methane
added in the following way

Genbox  -cs  water.gro  -ci    methane.pdb -nmol 4 -box 2 2 2 -o out.gro

When I run energy minimization 

grompp -np 2 -f em.mdp -p meth.top -c out.gro -o meth.tpr

mpirun -np 2 mdrun -s meth.tpr -o meth.trr -c out.gro -em.edr -g
meth.log


I have got the following message 

******
Steepest Descents converged to Fmax < 2000 in 100 steps
Potential Energy  = -1.1793982e+04
Maximum force     =  1.2537286e+03 on atom 1544
Norm of force     =            nan
******

In out.gro file some coordinates are nan, not a number.

It might be a problem due to overlap. 

Can you please let me know how to solve this problem?



Regards and thanks,

Jane


-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of David van der Spoel
Sent: Wednesday, 30 November 2005 6:54 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] NVT

Junfang.Zhang at csiro.au wrote:
> Dear Gromacs-users,
> 
>  
> 
> I am going to use Gromacs to simulate gas hydrates.
> 
> As I am new to this software, I am wondering if you can help me with 
> some questions.
> 
>  
> 
> Currently, I am looking at the system of water+methane. Can you please

> let me know how to keep the total number of molecules fixed or specify

> the number of water molecules and methane molecules?
> 
>  
> 
>  If I use the following command
> 
>  
> 
> Genbox  -cs  water.gro  -ci    methane.pdb -nmol 8 -box 2 2 2 -o
out.gro
> 
>  
> 
> to generate out.gro file, the number of methane molecules  can be 
> specified, but not the water molecules.
correct. Make a slightly larger box and manually remove the surplus 
water from the gro file.

> 
>  
> 
>  
> 
> Your assistance will be deeply appreciated.
> 
>  
> 
> Regards and thanks,
> 
>  
> 
>  
> 
> Jane
> 
>  
> 
>  
> 
>  
> 
>  
> 
> 
>
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> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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