Hi,
I think I have asked this question earlier in the forum .. that during my
3ns simulation of a 230 amino acid proteins some portion of 2 beta strands
got converted to loop/random coil, after visualizing in VMD. I checked the
DSSP profile also .. and as per the DSSP results it's coil in that
Dear Carsten Kutzner,
First off, thanks. I did not specify it in the input md.mdp file, but when I
looked at the generated out.mdp it had a Linear center of mass removal for the
groups [system].
When I added the pull vector it works, untill the two subunits crash(move past
a realistic
bharat gupta wrote:
Hi,
I think I have asked this question earlier in the forum .. that during
my 3ns simulation of a 230 amino acid proteins some portion of 2 beta
strands got converted to loop/random coil, after visualizing in VMD. I
checked the DSSP profile also .. and as per the DSSP
Thanks for ur kind reply Justin ...
I also searched the gmx userlist regarding the same query and I found out
that It was mentioned to repeat the simulation again with a different force
field .. but I don't know about the energy minimization parameters as I am
following ur lysozyme tutorial for
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:
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:
Thanks for such a detailed reply to my queries .. But conducting a 50ns
simulation will take time ... so i want to conduct independent simulation
and for that I searched some threads but was not able to get the proper
description and method... if u can guide me through an appropriate link ..
it
bharat gupta wrote:
Thanks for such a detailed reply to my queries .. But conducting a 50ns
simulation will take time ... so i want to conduct independent
simulation and for that I searched some threads but was not able to get
the proper description and method... if u can guide me through an
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
Sorry to ask this question but setting the gen_vel=yes and gen_seed = -1
will eventually lead to different simulation and thus different simulated
structures ?? .. and after completing one set of simulation with this
paramter and 3ns time .. do i have to repeat it some 3 or more times ??
pls
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
bharat gupta wrote:
Sorry to ask this question but setting the gen_vel=yes and gen_seed = -1
will eventually lead to different simulation and thus different
simulated structures ?? .. and after completing one set of simulation
with this paramter and 3ns time .. do i have to repeat it some 3
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,
Sorry to make this point here but running a 50ns simulation will take
roughly 1 month on my system but a 10ns simulation will take 5 days on my
system .. so would a 10ns be enough to monitor such motions .. also i
request to u guide me to a link where I can find more about this independent
bharat gupta wrote:
Sorry to make this point here but running a 50ns simulation will take
roughly 1 month on my system but a 10ns simulation will take 5 days on
A month is a reasonable time investment for quality MD simulations.
my system .. so would a 10ns be enough to monitor such
Anyways thanks for ur detailed answers .. After completing the simulation ,
the 10ns one I will get back to u if any doubt arises .. Also I am running a
3ns simulation of the same variant of GFP but with a different FF ... hoping
to get any positive result for that one ...
On Wed, Feb 2, 2011 at
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
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
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
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
Thanks a lot!!!
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
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
Ok and which definition have you used? the previous one with 5 atom
for molecule?
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
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
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
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
Dear all,
I have to perform a simulation in which a protein with a ligand is
included in a lipid bilayer+water. In the Justin Lemkul's tutorial on
membrane simulations, I see that the chosen forcefield is Gromos96 53a6
manually corrected to include the Berger lipids parameters. However, to
create
On 30/01/11 16:13, David van der Spoel wrote:
On 2011-01-30 17.08, ms wrote:
Since I have exactly the same needs (charged system in vacuum) I jump
in...
In http://www.gromacs.org/Documentation/Errors
it says:
Note for PME users: It is possible to use a uniform neutralizing
background charge
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
On 30/01/11 16:13, David van der Spoel wrote:
On 2011-01-30 17.08, ms wrote:
On 30/01/11 15:41, David van der Spoel wrote:
Since I have exactly the same needs (charged system in vacuum) I jump
in...
In http://www.gromacs.org/Documentation/Errors
it says:
Note for PME users: It is possible to
anna.marabo...@isa.cnr.it wrote:
Dear all,
I have to perform a simulation in which a protein with a ligand is
included in a lipid bilayer+water. In the Justin Lemkul's tutorial on
membrane simulations, I see that the chosen forcefield is Gromos96 53a6
manually corrected to include the Berger
Hello!
I want to use improper type 4 in the top file, but this is not working. When I
switch to type 2 everything is fine. What is the problem with type 4?
Regards,
Thomas
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The problem is solved with grompp i.e. I use the -t .cpt option. However,
now appending does not work. I remember Mark said in a previous mail that a
certain environment variable can allow appending to happen even in such
cases. I would liek to try that out.
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gmx-users mailing list
On 3/02/2011 6:15 AM, Sai Pooja wrote:
The problem is solved with grompp i.e. I use the -t .cpt option.
However, now appending does not work. I remember Mark said in a
previous mail that a certain environment variable can allow appending
to happen even in such cases. I would liek to try that
On Wed, Feb 2, 2011 at 3:15 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 3/02/2011 6:15 AM, Sai Pooja wrote:
The problem is solved with grompp i.e. I use the -t .cpt option. However,
now appending does not work. I remember Mark said in a previous mail that a
certain environment variable
Sai Pooja wrote:
On Wed, Feb 2, 2011 at 3:15 PM, Mark Abraham mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au wrote:
On 3/02/2011 6:15 AM, Sai Pooja wrote:
The problem is solved with grompp i.e. I use the -t .cpt option.
However, now appending does not work. I
On Wed, Feb 2, 2011 at 6:49 PM, Sai Pooja saipo...@gmail.com wrote:
Thanks Justin for being so patient. I have understood almost everything and
I hope this is the last question on this thread.
See inline ...
On Wed, Feb 2, 2011 at 5:53 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Sai
Sai Pooja wrote:
Thanks Justin for being so patient. I have understood almost everything
and I hope this is the last question on this thread.
See inline ...
On Wed, Feb 2, 2011 at 5:53 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Sai Pooja wrote:
On
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