[gmx-users] SS bond forcing
pithevenet at free.fr
Tue Apr 10 15:03:31 CEST 2012
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.
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 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
> gmx-users mailing list gmx-users at gromacs.org
> 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...
More information about the gromacs.org_gmx-users