[gmx-users] SS bond forcing

[Justin A. Lemkul]

Pierre THEVENET wrote:
> 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.
> 

I can't predict how much time it would take.  How far apart are the S atoms from 
one another?  If it's just a small distance beyond the normal cutoff, it should 
be quick, a few hundred ps or less (assuming everything else is otherwise 
stable).  If the distance is very long and would require large structural 
transitions to accommodate, then you're probably in trouble.

-Justin

> 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 <mailto:jalemkul at vt.edu>>
> 
> 
> 
>     pithevenet at free.fr <mailto: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 <http://vt.edu> | (540) 231-9080
>     <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
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-- 
========================================

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

========================================