[gmx-users] Re: gmx-users Digest, Vol 105, Issue 43

[SANTU BISWAS]

thank you Justin.Now it is fine.

> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 9 Jan 2013 22:50:13 +0530
> From: SANTU BISWAS <santu.biswas85 at gmail.com>
> Subject: [gmx-users] energy-mimisation-problem
> To: gmx-users at gromacs.org
> Message-ID:
>         <CAEwZ1z-7yV_8DcAUrT+rM6FkdqOmcMftXpdKbzL0atyYOorrsQ at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> dear users,
>
>               I am performing an energy minimization of
> apolypeptide(formed by alanine-10-residues) in vacuum box by using
> Steepest Descent(initially) and then Conjugate Gradient methods in
> gromacs_4.5.5_doubleprecision.The chain length of
> alanine-10-mer is around 1.5 nm.Here i want to see only the sort-range
> interactions.so i use cutoff 2.0 nm .But in the
> output (.log )file there is a contribution of energy for long-range
> interactions(in both energy minimisation methods).
> I do not understand why this is happening.
>
> the input file for energy minimisation is,
>
> ;title                    =
> cpp                      = /lib/cpp
> ;include                  =-I../top/
> define                   = -DFLEXIBLE
> ;         Input file
> integrator              =  steep/cg
> nsteps                  =  10000
> nstlist                 =  1
> rlist                   =  1.0
> rcoulomb                =  2.0
> rvdw                    =  2.0
> ;         Energy minimizing stuff
> emtol                   =  0.001
> emstep                  =  0.1
> nstcgsteep              =  10
>
>
> the output(.log )file is,
>
>  Energies (kJ/mol)
>            Bond          Angle            Proper Dih.
> Ryckaert-Bell.          LJ-14
>     8.48244e+00    2.10205e+01    2.39409e+00           9.86941e+01
>      1.47894e+02
>      Coulomb-14        LJ (SR)        LJ (LR)          Coulomb (SR)
> Coulomb (LR)
>     1.63221e+03   -1.64038e+02   -4.97232e-01   -3.00455e+03   -1.00138e+01
>       Potential       Pressure (bar)
>    -1.26841e+03    0.00000e+00
>
> ........
> santu
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 09 Jan 2013 12:30:06 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] energy-mimisation-problem
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <50EDA91E.2070306 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 1/9/13 12:20 PM, SANTU BISWAS wrote:
>> dear users,
>>
>>                I am performing an energy minimization of
>> apolypeptide(formed by alanine-10-residues) in vacuum box by using
>> Steepest Descent(initially) and then Conjugate Gradient methods in
>> gromacs_4.5.5_doubleprecision.The chain length of
>> alanine-10-mer is around 1.5 nm.Here i want to see only the sort-range
>> interactions.so i use cutoff 2.0 nm .But in the
>> output (.log )file there is a contribution of energy for long-range
>> interactions(in both energy minimisation methods).
>> I do not understand why this is happening.
>>
>> the input file for energy minimisation is,
>>
>> ;title                    =
>> cpp                      = /lib/cpp
>> ;include                  =-I../top/
>> define                   = -DFLEXIBLE
>> ;         Input file
>> integrator              =  steep/cg
>> nsteps                  =  10000
>> nstlist                 =  1
>> rlist                   =  1.0
>> rcoulomb                =  2.0
>> rvdw                    =  2.0
>> ;         Energy minimizing stuff
>> emtol                   =  0.001
>> emstep                  =  0.1
>> nstcgsteep              =  10
>>
>>
>
> You haven't set a value for the pbc keyword, so it takes the default value
> (xyz).  The result is that you're not really minimizing in vacuo, but rather in
> some sort of pseudo-crystal state that probably has lots of periodicity
> artifacts.  That's probably the source of the energy terms - your peptide
> interacting with itself.
>
> -Justin
>
>> the output(.log )file is,
>>
>>   Energies (kJ/mol)
>>             Bond          Angle            Proper Dih.
>> Ryckaert-Bell.          LJ-14
>>      8.48244e+00    2.10205e+01    2.39409e+00           9.86941e+01
>>       1.47894e+02
>>       Coulomb-14        LJ (SR)        LJ (LR)          Coulomb (SR)
>> Coulomb (LR)
>>      1.63221e+03   -1.64038e+02   -4.97232e-01   -3.00455e+03   -1.00138e+01
>>        Potential       Pressure (bar)
>>     -1.26841e+03    0.00000e+00
>>
>> ........
>> santu
>>
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>