[gmx-users] Difference in the Forcefields and speed...

[sharada]

Hello,
Thankyou Drs Mark Abraham and Caterina Arcangeli for the useful suggestions.  They  worked for me.  I could cat the two trr files and calculate the backbone g_rms values.  I have to yet see how much they deviate with the original structures. I have couple of questions:
If I do the MD studies using Gromacs 3.1 and Gromacs 3.3 with differennt forcefields like ffg43a1 and ffG53a5 respectively in the same simulating conditions how different would be my results ? or will there be any difference ?
Is there a difference  in the speed of the simulations say if I run them on SGI Octane R12000 and a Personal computer with 512 RAM Pentium III ? Incidently Gromacs 3.1 is loaded on Octane and Gromacs 3.3 on Pentium III .
Why I am asking the second question is that the time taken on Octane is much larger ( around 9 days) compared to the Pentium III (3 days) what may be the reason ? 
Thanks for the patience ...
regards
A .Sharada  Devi
Technical Officer C
Center for Cellular Molecular 
Biology
Habsiguda Uppal Road
Hyderabad -500007
India 
-- Original Message --
From: Caterina Arcangeli <caterina.arcangeli at casaccia.enea.it>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Wed, 03 Jan 2007 10:11:45 +0100
Subject: Re: [gmx-users] (no subject)
Hi,
using the command:
trjcat -f nchnp3_5npep.trr nchnp3_10pep.trr -o nchnp3_15pep.trr -settime
the program will ask you the start time of each file. Try putting "5001"
for the first file and "c" (continue) for the second file.
It should be work.
Ciao
Caterina
Mark Abraham wrote:
> sharada wrote:
>> Hello gmx_users,
>>
>> I wish you a very happy and prosperous new year 2007.  I have a very
>> fundamental question in trjcat usage. I have two *.trr files of 5ns
>> and 10 ns runs . I  would like to concanate the two and make a 15ns
>> trr file. How to give the command so that the starting time of the
>> 10ns file should be 5001ps and not 0ps and end time is 15000ps and not
>> 10000 ps.  May this is a trivial question. Kindly help.  I have tried
>> using the following command :
>> trjcat -f nchnp3_5npep.trr nchnp3_10pep.trr -settime -o
>> nchnp3_15pep.trr -b 0.00 -e 15000
> 
> It's just like the command line utility cat... it will do a straight
> concatenation.
> 
> trjcat -f 5n.trr 10n.trr -o 15n.trr
> 
> should do what you want.
> 
> Check using gmxdump , of course
> 
> Mark
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-- 
Caterina Arcangeli
ENEA, Computing and Modelling Unit (CAMO)
Casaccia Research Center - Post Bag 026
Via Anguillarese 301 - 00060 Roma
phone +39 06.3048.6898
fax   +39 06.3048.6860
http://www.enea.it
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