[gmx-users] RE: NEMD

[Junfang.Zhang at csiro.au]

Hi David,

Thank you very much for your reply.

I am going to be involved in two research projects, gas hydrates and
clay swelling, by using Gromacs.

As I am new user of Gromacs, I am wondering if you can give me some
advice on the following questions:

Non-equilibrium MD (NEMD) simulation of clay swelling:  two-half
negatively charged clay layer in the simulation box, which is fixed.
Water molecules and cations between the clay layers will flow. Can you
please let me know how to perform non-equilibrium MD simulation by using
Gromacs? Where to specify the parameters for NEMD?

As the external force will be introduced, the viscous heat should be
removed from the system. Since the clay layers are fixed, do I have to
thermostat the fluids between the walls?

Your suggestions will be deeply appreciated.

Best wishes 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: Thursday, 1 December 2005 7:03 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] NVT

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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>  
>
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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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