Sorry, but changing the definition and using the other suggested by
Dimitris doesn't change the results, I still have the same problem in
minimisation...
Valerio
Dimitris Dellis ha scritto:
On 02/02/2011 07:47 PM, Justin A. Lemkul wrote:
Dimitris Dellis wrote:
Hi.
There is an issue w
On 02/02/2011 07:47 PM, Justin A. Lemkul wrote:
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 21 rC-H
1 31 rC-CL
1
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 21 rC-H
1 31 rC-CL
1 41 rC-CL
1 51 rC-C
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 21 rC-H
1 31 rC-CL
1 41 rC-CL
1 51 rC-CL
2 31 rH-
The dynamic works, but I still have the same problems with minimization...
"Justin A. Lemkul" 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" ha scritto:
vferra...@units.it
vferra...@units.it wrote:
Ok and which definition have you used? the previous one with 5 atom for
molecule?
Yes.
-Justin
"Justin A. Lemkul" 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... Th
Ok and which definition have you used? the previous one with 5 atom
for molecule?
"Justin A. Lemkul" 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 po
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
Just the last thing... can you copy your mdp file? I think I'm having
some problems also with that... Thanks.
Valerio
"Justin A. Lemkul" ha scritto:
Justin A. Lemkul wrote:
I've obtained a stable trajectory for a single CHCL3 molecule. By
setting "continuation = no" (so that constr
Thanks a lot!!!
Valerio
"Justin A. Lemkul" ha scritto:
Justin A. Lemkul wrote:
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
Justin A. Lemkul wrote:
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 t
Justin A. Lemkul wrote:
vferra...@units.it wrote:
No, is not working also in this case... probably the problem is with
my mdp files:
I would argue that it's the coordinates that are the problem. For
instance, compare the distances expected by the topology:
1 3 1 0.175
vferra...@units.it wrote:
No, is not working also in this case... probably the problem is with my
mdp files:
I would argue that it's the coordinates that are the problem. For instance,
compare the distances expected by the topology:
1 3 1 0.1758
1 4 1 0.1
No, is not working also in this case... probably the problem is with
my mdp files:
for minimization is:
title = Minimization
cpp = /lib/cpp
include = -I../top
constraints = none
integrator = steep
emtol = 5.0
emstep = 0.01
nsteps
vferra...@units.it wrote:
Seems that the new definition I've found works, but it is still unclear
to me why...
There was a post long ago that I seem to remember reported the same problem.
Since there is no true bond between H and C, the H position is basically
triangulated by all of the o
Seems that the new definition I've found works, but it is still
unclear to me why...
Valerio
vferra...@units.it ha scritto:
The molecule is rigid because it's all constrained and the
coordinates of the single molecule seem to be ok:
CLF
5
1CLFCCl1 3.041 1.571 0.924
The molecule is rigid because it's all constrained and the coordinates
of the single molecule seem to be ok:
CLF
5
1CLFCCl1 3.041 1.571 0.924
1CLFHCl2 3.001 1.637 0.845
1CLFCL13 3.071 1.661 1.073
1CLFCL24 3.186 1.493 0.
Justin A. Lemkul wrote:
vferra...@units.it wrote:
I've just tried with a single CHCL3 molecule, here's the output:
Back Off! I just backed up md.log to ./#md.log.2#
Getting Loaded...
Reading file clfmin.tpr, VERSION 4.0.7 (single precision)
Loaded with Money
NNODES=2, MYRANK=1, HOSTNAME=bi
vferra...@units.it wrote:
I've just tried with a single CHCL3 molecule, here's the output:
Back Off! I just backed up md.log to ./#md.log.2#
Getting Loaded...
Reading file clfmin.tpr, VERSION 4.0.7 (single precision)
Loaded with Money
NNODES=2, MYRANK=1, HOSTNAME=biohazard
NODEID=1 argc=6
Mak
I've just tried with a single CHCL3 molecule, here's the output:
Back Off! I just backed up md.log to ./#md.log.2#
Getting Loaded...
Reading file clfmin.tpr, VERSION 4.0.7 (single precision)
Loaded with Money
NNODES=2, MYRANK=1, HOSTNAME=biohazard
NODEID=1 argc=6
Making 1D domain decomposition 2
vferra...@units.it wrote:
Dear all,
I'm dealing with a simulation of a polymer in CHCL3, the polymer works
good, but I have some problems with the CHCL3 definition in GROMOS 53a6 ff.
I've taken the CHCL3 definition from the automated topology builder
website:
http://compbio.biosci.uq.edu.au
Dear all,
I'm dealing with a simulation of a polymer in CHCL3, the polymer works
good, but I have some problems with the CHCL3 definition in GROMOS
53a6 ff.
I've taken the CHCL3 definition from the automated topology builder website:
http://compbio.biosci.uq.edu.au/atb/download.py?molid=1597
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