[gmx-users] Re: gmx-users Digest, Vol 108, Issue 140

[Arunima Shilpi]

hello sir

there was error in running grompp file of umbrella sampling... the error it
says

"no such molecule type sol" found.......

how to debug the error




On Tue, Apr 23, 2013 at 3:30 PM, <gmx-users-request at gromacs.org> wrote:

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> Today's Topics:
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>    1. Re: Fwd: Selecting the temperature distribution (massimo sandal)
>    2. Tabulated non-bonded potentials - regd (ramesh cheerla)
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 23 Apr 2013 11:21:30 +0200
> From: massimo sandal <devicerandom at gmail.com>
> Subject: Re: [gmx-users] Fwd: Selecting the temperature distribution
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>         <
> CAGqFyor4rgnGcveaOzUj7VDtk3j0HjWE1yiVN+jUMcy-DB_CrQ at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Look here: http://folding.bmc.uu.se/remd/
>
>
>
> 2013/4/23 bharat gupta <bharat.85.monu at gmail.com>
>
> > Dear gmx users,
> >
> > I am planning to run REMD for a peptide (406 atoms )+ solvent system
> > (27639). The temperature range I selected is from 300 to 500. I want to
> > select appropriate temp. for 56 replicas. I randomly chose some temp
> > distribution and the exchange probabilities was 0.0. I know that we can
> use
> > the formula  Ti=T0*ek*i, but what is the value for i and K here ??
> >
> > --------
> > BHARAT
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> ------------------------------
>
> Message: 2
> Date: Tue, 23 Apr 2013 14:59:59 +0530
> From: ramesh cheerla <rameshgromacs at gmail.com>
> Subject: [gmx-users] Tabulated non-bonded potentials - regd
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>         <
> CAPNFZqe6E4UcQSzQbMcT4j0sUomwQZ4_Yge_sSx4EGps47iy_Q at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear Gromacs users,
>
>       In forcefield of  my system, I have non-bonded function of the form U
> = A*exp(-Brij) - C/(rij^6) - D/(rij^4),  for this I wanted to use tabulated
> potentials. I have defined functions f(r), g(r) and  h(r)  as the
> following,
> f = 1/r;
> fprime = 1/(pow(r,2));
> g = (C*(-1/(pow(r,6))));
> gprime = (-6*C/(pow(r,7)));
> h = A*exp(-B*r);
> hprime = ((A*B)*(exp(-B*r)));
>       Then I have tabulated all these  with a bin size (dr) of 0.002 nm and
> given "nbfunc" as 1 in forcefield.itp and provided "C" and "A" as 1 in
> ffnonbonded.itp (As I have used A,B & C values in generation of table
> itself) . I have generated one such table for each  interaction.  While
> running simulations with these tables  I am getting the following warning:
>
> "WARNING: For the 3999 non-zero entries for table 2 in table.xvg the forces
> deviate on average 78% from minus the numerical derivative of the
> potential"
> After this job is crashing with error  "Segmentation fault"
> 1) Can anybody please tell me the reason for the above Warning  and how one
> can rectify it ?
> 2) Can I define the functions for the above mentioned  non-bonded function
> like this ?
> I have checked potential energy of model system (single point energy
> calculations i.e., zero step MD and the one that  obtained from the code
> that I have written, both are matching.
> I am using GROMACS version 4.5.5 and also tested the same thing in V 4.6.
>
> Can anybody help me in this regard,
>
> Thank you in advance.
>
> Regards,
> Ramesh.
>
>
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> End of gmx-users Digest, Vol 108, Issue 140
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>


-- 

Thanking You with Regards.

Arunima Shilpi

Ph. D Research Scholar(Cancer & Epigenetics)
Department of Life Science
National Institute of Technology
Rourkela
Odisha