[gmx-users] NVT

[David van der Spoel]

Junfang.Zhang at csiro.au wrote:

>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?
>  
>
Start with a lower density solvent.
Editconf -density 500 -f spc216.gro -o out.gro
minimize out.gro and then add  methane.



>
>
>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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>
>
>  
>


-- 
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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