From: abhijit ramachandran (abhi_adroit_at_yahoo.com)
Date: Tue Mar 24 2009 - 10:44:47 CDT
Hi Peter,
Thanks for the reply,
Let me see if i can get something done, i dont have much Gromacs knowledge, but thanks for the guidance.
My colleague was working on Gromacs and he was not sure that the behavior observed there was something that is expected, so we basically decided to test in NAMD since i am a little familiar with it. Since he has just begun working there we wanted to see if the files generated by him are correct, and there are no configuration file parameters that he has added or removed which affect the system.
Thanks again.
Regards,
Abhijit
abhijit.ramachandran_at_gmail.com
________________________________
From: Peter Freddolino <petefred_at_ks.uiuc.edu>
To: abhijit ramachandran <abhi_adroit_at_yahoo.com>; namd-l <namd-l_at_ks.uiuc.edu>
Sent: Monday, 23 March, 2009 10:43:27 PM
Subject: Re: namd-l: Gromacs simulation not running in NAMD
Hi Abhijit,
I know that the namd gromacs file reader is not complete; I've run into
cases like this as well, but am not aware of anyone taking it upon
themselves to improve it further (it would need to be someone who knows
the gromacs file formats well). I have done runs in gromacs and namd
using equivalent parameters (albeit reformatted) and gotten equivalent
results in the past.
Can I ask, why do you feel the need to confirm the results you got from
gromacs in namd?
Peter
abhijit ramachandran wrote:
> Hi all,
>
> I was trying to run a gromacs simulation on namd but did not succeed to
> get it working, i have seen many unanswered previous questions, like
> this one
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/2527.html, was
> hoping someone answers this, has anyone run a simulation which runs in
> gromacs and then run in NAMD and obtained the same results. I get the
> following error
>
> Syntax error <0 args> in ANGELS: #include "DNA.itp"
>
> Below is DNA.top file, which i had mentioned in my run file as
> grotopfile. *This simulation is working in gromacs,* but i wanted to
> confirm the results in NAMD but not able to run it here, any suggestions
> welcome.
>
> I tried removing the include statement mentioned here and copy pasted
> the .itp file into this .top file, then the error changed and the error was
>
> MOLECULE DNA is UNDEFINED
>
> Is the error, since the # is used for statements that are to be
> discarded in NAMD scripts, but # is used with 'include' to get
> the header files, so I have no idea why its giving this error.
>
> This is the .top file
>
> #include "DNA.itp"
>
> [ system ]
> ; name
> MODEL CYLINDER
> [ molecules ]
> ; name number
> DNA 1
> NA 19
> CL 19
> W 5
>
> *This is my config file:*
>
> gromacs on
> grotopfile dna.top
> grocoorfile dna.gro
>
> numsteps 10000
> outputName eq0
> XSTfile eq0.xst
> minimization on
> temperature 0
> cellBasisVector1 33.0 0.0 0.0
> cellBasisVector2 0.0 33.0 0.0
> cellBasisVector3 0.0 0.0 33.0
> cellOrigin 0.0 0.0 0.0
> switching on
> switchDist 10
> cutoff 12
> pairlistdist 14
> margin 3
> binaryOutput yes
> binaryRestart yes
>
> paraTypeCharmm on
> wrapAll yes
> wrapNearest yes
> COMmotion no
> outputEnergies 100
> outputTiming 100
> xstFreq 100
> dcdFreq 100
> restartFreq 100
> timestep 0.5
> nonBondedFreq 2
> fullElectFrequency 4
> stepsPerCycle 20
> Pme on
> PmeGridSizeX 48
> PmeGridSizeY 48
> PmeGridSizeZ 48
> exclude scaled1-4
> 1-4scaling 1
> Thanks in advance
>
> Regards,
>
> Abhijit
> abhijit.ramachandran_at_gmail.com <mailto:abhijit.ramachandran_at_gmail.com>
>
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