[gmx-users] peptide coming out of the box

[andrea spitaleri]

Hi,
why do not think about a beginners mailing list or gromacs for dummies?
of course this is my humble opinion to you guys ....
and of course  I agree with you in searching **always before** in the list archive ..
This is just a suggestion ...

Regards,

andrea

Berk Hess wrote:
> Maybe we should let people do a test before they can become member
> of the mailing list. We already have two questions:
> Can you search the list archive?
> It is a problem when a peptide comes out of the box?
> 
> Berk.
> 
>> From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
>> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>> Subject: Re: [gmx-users] peptide coming out of the box
>> Date: Tue, 20 Mar 2007 11:30:18 +0100
>>
>> Oh no.., not again!
>>
>> Read the manual, browse the archives and try to understand periodic
>> boundary conditions!
>> (and use trjconv -fit translate or trjconv -center on your trajectory)
>>
>> Tsjerk
>>
>> On 3/20/07, priya priya <priyaanand_27 at yahoo.co.in> wrote:
>>> Dear all
>>>
>>>  I started with 6 residue peptide simulation in water for 1ns.
>>> initially i
>>> placed the peptide in the center using the command editconf -c flag, but
>>> after MD peptide is coming out of the water box. I want to calculate the
>>> water molecules around it and peptide interactions with water.
>>>
>>>  Is there an error running simulation.
>>>  Regards
>>>  Priya
>>>
>>>
>>>  ________________________________
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>>>
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>>
>>
>> -- 
>> Tsjerk A. Wassenaar, Ph.D.
>> Junior UD (post-doc)
>> Biomolecular NMR, Bijvoet Center
>> Utrecht University
>> Padualaan 8
>> 3584 CH Utrecht
>> The Netherlands
>> P: +31-30-2539931
>> F: +31-30-2537623
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
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> 
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-- 
-------------------------------
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom/
-------------------------------

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