[gmx-users] solvent box

[Chng Choon Peng]

Hi Sadhna,
    
    Alternatively, you might need to remove translations during your
MD simultion. Try adding:
nstcomm             =  1
comm_grps           =  Protein
comm_mode           =  Linear ; added to remove translation.

In your MDP file.

I faced a similar problem before and I think editconf with "-c" only centers
the box before the simulation.
I keep using larger box sizes before I realized it's center-of-mass motion.
However, I've not been able to remove rotations which is said to be ok in
solvent.


cheers,
Choon-Peng

-- 
Mr. Choon-Peng CHNG
Research Associate
BioInformatics Institute, BMSI, A*STAR
30 Biopolis Street
#07-01 Matrix Building
Singapore 138671
Tel (O): +65 64788301 Fax (O): +65 64789047
www.bii.a-star.edu.sg/~cpchng


On 2/12/04 2:47 PM, "Stud_Psychopharm" <stu_psyc at nimhans.kar.nic.in> wrote:

> sadhna, you can try with this command
> editconf -f input.gro -d 0.8 -c -o output.gro
> 
> hope you might not given -c command in your job..  I had the same
> problem, it worked out after giving "-c" at editconf command..
> all the best
> ------------------------------------------------------------
> "The more we learn the more we realize how little we know." -
> R.Buckminster Fuller
> 
> Blaise M.
> Graduate Student,
> Department of Psychopharmacology,
> National Institute of Mental Health And Neuro Sciences (NIMHANS),
> Bangalore-560029,
> India. Tel: 91 80 6995112.
> 
> 
> -----Original Message-----
> From: sadhna <sadhana at che.iitb.ac.in>
> To: <gmx-users at gromacs.org>
> Date: Thu, 12 Feb 2004 11:50:21 -0500 (GMT)
> Subject: [gmx-users] solvent box
> 
>> hi all,
>>        While doing MD in water my peptide is not confined to the centre
>> of the box and sometimes a part of the peptide also goes out of the
>> box,
>> though i have used box size of appropriate length. where could be the
>> problem?
>> 
>> thanks in advance
>> sadhna
>> 
>> Sadhna Joshi
>> Research Scholar
>> Dept of Chemical Engg
>> Indian Institute of Technology,Powai
>> Mumbai-400076
>> India
>> 
>> 
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