2013/3/25 Mercadante, Davide <davide.mercada...@h-its.org>:
> Dear Christoph,
>
> Many thanks for your reply that I have very much appreciated.
>
> No, nothing so top secrets. I am just trying to reproduce the full atom
> Potential Mean Force (PMF) of a protein in a CG fashion so that we could
> scale up the simulation in terms of system size. Other coarse grained ff
> have failed reproducing the Full atom PMF and it looks that votca can
> finally do the job..however, one of my question is if I would have a
> potential that is conformation-dependent. For example: if I have two
> conformations 1) extended 2) collapsed of the same peptide, will I have
> two different (or very different) potentials (reflected in the topologies)
> because my full atom simulations were performed on different
> conformational ensembles? I hope not as the forcefield should be
> conformation-independent right?
I not the expert for coarse-graining of peptides, maybe somebody else
can comment on that, but if you average over both ensembles you will
get a force filed which possibly works in both cases.
See:
Hills RD Jr, Lu L, Voth GA (2010) Multiscale Coarse-Graining of the
Protein Energy Landscape. PLoS Comput Biol 6(6): e1000827.
doi:10.1371/journal.pcbi.1000827
and
Olga Bezkorovaynaya, Alexander Lukyanov, Kurt Kremer, Christine Peter
DOI: 10.1002/jcc.22915
>
> It would be nice if you could post your script so that I can sort of
> create a list automatically and then work manually on the ranges.
I put it into one file:
#!/bin/bash
beads=( A B C )
echo "<cg>"
for ((i=0;i<${#beads[@]};i++)); do
for ((j=$i;j<${#beads[@]};j++)); do
cat <<EOF
<non-bonded>
<name>${beads[$i]}-${beads[$j]}</name>
<type1>${beads[$i]}</type1>
<type2>${beads[$j]}</type2>
<min>0</min>
<max>0.9</max>
<step>0.01</step>
<inverse>
<target>${beads[$i]}-${beads[$j]}.dist.tgt</target>
<gromacs>
<table>table_${beads[$i]}_${beads[$j]}.xvg</table>
</gromacs>
</inverse>
</non-bonded>
EOF
done
done
echo "</cg>"
>
> Thank you very much for your time.
>
> Cheers,
> Davide
>
>
>
>
>
> On 25/03/13 4:38 PM, "Christoph Junghans" <jungh...@votca.org> wrote:
>
>>2013/3/25 Mercadante, Davide <davide.mercada...@h-its.org>
>>>
>>> Dear Christoph,
>>>
>>> I am writing because I have a question about preparing my system for CG
>>>simulations using votca.
>>Welcome, and please if your research is not top-secret, post your
>>questions on our mailing list: <votca@googlegroups.com>, so that
>>others can learn from it.
>>>
>>> I want to simulate a peptide in water using a CG approach and I was
>>>thinking of using votca to determine the non-bonded and bonded CG
>>>potentials starting from the full atom simulations that I have already
>>>performed on the same system (using Gromacs ersion 4.5.5). In order to
>>>do this I have studied the votca manual and I found it very interesting.
>>>I am interested to apply Boltzmann inversion method to find out bonded
>>>potential and IBI to determine the bonded potential in order to build a
>>>gromacs topology to use in further simulations.
>>>
>>> However, I have a question about calculating the non-bonded potential.
>>>It seems to me that I have to "feed" votca with a settings.xml file that
>>>lists all the non-bonded interactions occurring and other parameters to
>>>carry out IBI. However, in my system (not very small) the list of
>>>non-bonded interactions will be possibly very long..there is an
>>>automated way to build the settings file? How I can get a list of
>>>non-bonded interactions in my system?
>>
>>I am sorry to tell you that there is no automated way to create these
>>xml files, we thought about that several times, but as it can be done
>>with a 10 line shell script and most interactions will have different
>>ranges, which will need some tweaking anyhow, we never wrote a program
>>to do it.
>>
>>I can post my script if you need it!
>>
>>Cheers,
>>
>>Christoph
>>
>>>
>>> Thank you in advance for your time and please accept my apologies if
>>>this is a stupid question. I am a newbie of votca.
>>>
>>> Cheers,
>>> Davide
>>>
>>> **********************************************
>>> Davide Mercadante Ph.D.
>>> Postdoctoral Fellow
>>> Heidelberg Institute for Theoretical Studies HITS
>>> Schloss-Wolfsbrunnenweg, 35
>>> D-69118 Heidelberg, Germany.
>>> **********************************************
>>>
>>> --
>>> Christoph Junghans
>>> Web: http://www.compphys.de
>
--
Christoph Junghans
Web: http://www.compphys.de
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