Dimitris Dellis wrote:
Hi.
There is an issue with constraints.
H atom position is not uniquely defined with the constraints you use.
Try these constraints (substitute symbols with numbers)
1 2 1 rC-H
1 3 1 rC-CL
1 4 1 rC-CL
1 5 1 rC-CL
2 3 1 rH-CL
2 4 1 rH-CL
3 4 1 rCL-CL
3 5 1 rCL-CL
4 5 1 rCL-CL
I suggested this solution long ago, but Berk said it was an incorrect approach:
http://redmine.gromacs.org/issues/359
-Justin
DD
On 02/02/2011 06:20 PM, vferra...@units.it wrote:
The dynamic works, but I still have the same problems with
minimization...
"Justin A. Lemkul" <jalem...@vt.edu> ha scritto:
vferra...@units.it wrote:
Ok and which definition have you used? the previous one with 5 atom
for molecule?
Yes.
-Justin
"Justin A. Lemkul" <jalem...@vt.edu> ha scritto:
vferra...@units.it wrote:
Just the last thing... can you copy your mdp file? I think I'm
having some problems also with that... Thanks.
For EM, I used the .mdp file you posted in your first message and
added the line "continuation = yes." For MD, I changed nstlist
from 100 to 5.
-Justin
Valerio
"Justin A. Lemkul" <jalem...@vt.edu> ha scritto:
Justin A. Lemkul wrote:
<snip>
I've obtained a stable trajectory for a single CHCL3 molecule.
By setting "continuation = no" (so that constraints are not
solved before step 0) in the em.mdp file, and then reducing
nstlist to 5 in md.mdp, I
Ack, this should be "continuation = yes." Sorry for the
confusion. I will copy from my .mdp file...I will copy from my
.mdp file... :)
-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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
