[gmx-users] SS bond forcing

[Pierre THEVENET]

How long the MD simulation should be? The problem is that I run multiple
simulation (a hundred at a time) and the MD are really time consuming. I
should probably can't do it, if the time you propose is too long, I
probably forget it.

Thank you

--------------------------

Pierre THEVENET
Ph.D. Candidate
INSERM - MTi
Ecole Doctorale B3MI
Université Paris Diderot - Paris 7




2012/4/10 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> pithevenet at free.fr wrote:
>
>>
>> Here is what I have done:
>>
>> First, I created the .gro file with the command line:
>> pdb2gmx  -f test.pdb  -o test.gro  -p test.top -ignh -missing
>>
>>
>> Then, I added at the end of my test.top file the following lines (I
>> double checked the atom numbers):
>>
>> [ distance_restraints ]
>> ; ai aj type index type' low up1 up2 fac
>>  37 140 1   0     1     0.19 0.21 0.22 1
>>
>> then, I done:
>> editconf -f test.gro -o test-box.gro -d 2.0 -c -bt cubic
>>
>> grompp -c test-box.gro -p test.top -o test-min.tpr -f test-em.mdp
>>
>> mdrun -s test-min.tpr -c test-min.gro -deffnm test-min -v -nice 0
>>
>>
>> and finally get my new pdb file with:
>>
>> editconf -f test-min.gro -o test-min.pdb
>>
>> But it didn't seemed it had make the two sufur atom closer than if I
>> didn't add the distance_restrain in the top file.
>>
>> Did I do something wrong?
>>
>>
> Simple energy minimization is unlikely to give rise to the structural
> changes you need to bring these atoms close together.  Running a short MD
> simulation may work, though if the atoms are very far apart and you force
> them together quickly, you may have stability issues.
>
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120410/1348bdbc/attachment.html>