Hi,
I am trying to perform expanded ensemble simulations between 2 states A
(lambda=0) and B (lambda =1) with 6 intermediate lambda values.
In state B the Hamiltonian is rescaled, such that the epsilons of the vdW
interactions, the charges, the bond, angle and dihedral constants are a
multiple
at 4:04 PM, HANNIBAL LECTER
hanniballecte...@gmail.com
wrote:
Hi,
I am trying to perform expanded ensemble simulations between 2 states A
(lambda=0) and B (lambda =1) with 6 intermediate lambda values.
In state B the Hamiltonian is rescaled, such that the epsilons of the vdW
ref_p= 0.0 0.0 ??
Are you sure about this??
On Tue, Jun 11, 2013 at 12:08 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:
what happens to your energy before the observed crash? does the crash
happen at the same time-step each time?
Dr. Vitaly Chaban
On Tue, Jun 11,
It is not very clear as to what you are trying to do? If you have the final
coordinates and velocities from a previous simulation, I would recommend
start a simulation using the .gro file and ensuring that you have
gen-vel=no in the .mdp file.
If you have a well-equilibrated system, then the
You can do it by using simple shell scripting
On Jul 17, 2013 12:58 AM, Shine A shin...@iisertvm.ac.in wrote:
Sir,
Using g_cluster I clustered snapshots in md trajectory using the
command as follows
g_cluster -s sd_7.tpr -f traj7.trr -dist rmsd-distribution.xvg -o
clusters.xpm -sz
Hi,
I am trying to simulate nanotube (1156) with protein and water and I am
using Tcoupl = system using sd integrator in gromacs.
Since I am position restraining the nanotube, I would expect that the
restrained CNT degrees of freedom are accounted for while calculating the
system temperatures
Thanks. Is there any way to position restraint a part of the system while
keeping all bonds flexible?
On Fri, Aug 16, 2013 at 5:24 PM, Justin Lemkul jalem...@vt.edu wrote:
On 8/16/13 5:09 PM, HANNIBAL LECTER wrote:
Hi,
I am trying to simulate nanotube (1156) with protein and water and I
Hi,
I have been performing NPT simulations with CNT, Protein and water.
However, when I freeze the CNT, the system crashes with segmentation fault.
If I use position restraints, the temperature of the system is lower than
what it is expected to be. I am using sd coupling.
If I couple the
= yes
gen_temp= 300.000
gen_seed=981487
On Mon, Aug 19, 2013 at 11:35 AM, Justin Lemkul jalem...@vt.edu wrote:
On 8/19/13 11:32 AM, HANNIBAL LECTER wrote:
Hi,
I have been performing NPT simulations with CNT, Protein and water.
However, when I
I am performing NPT here but this artifact is independent of whether one is
using NPT or NVT.
On Mon, Aug 19, 2013 at 11:42 AM, HANNIBAL LECTER
hanniballecte...@gmail.com wrote:
Thanks Justin.
I am not sure how it is fundamentally incompatible. Especially with
refcoord-scaling = com. Can
I usually use 1.0 for my systems and I get the correct values for the
temperatures. If I couple it as a system, the low T-CNT yields a different
value than the target 300K.
On Mon, Aug 19, 2013 at 11:48 AM, Justin Lemkul jalem...@vt.edu wrote:
On 8/19/13 11:42 AM, HANNIBAL LECTER wrote
Interestingly, removing position restraints does not have much of an impact.
On Mon, Aug 19, 2013 at 1:40 PM, Justin Lemkul jalem...@vt.edu wrote:
On 8/19/13 11:58 AM, HANNIBAL LECTER wrote:
I usually use 1.0 for my systems and I get the correct values for the
temperatures. If I couple
, if md is used with SHAKE the system crashes with segmentation
fault. Does anyone have any idea as to what could be the problem?
On Mon, Aug 19, 2013 at 6:40 PM, HANNIBAL LECTER hanniballecte...@gmail.com
wrote:
Interestingly, removing position restraints does not have much of an
impact.
On Mon
from the hot to the cold freeze groups. I maybe missing
something.
On Wed, Aug 21, 2013 at 6:03 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
On Wed, Aug 21, 2013 at 10:22 PM, HANNIBAL LECTER
hanniballecte...@gmail.com wrote:
I am not sure what is the problem with using NPT, constraints
21, 2013 at 10:22 PM, HANNIBAL LECTER
hanniballecte...@gmail.com wrote:
I am not sure what is the problem with using NPT, constraints and
freezegroups. Unless there is some fundamental issue (which I cannot
think
of) one should in principle be able to run NPT with the CNT system
probably u do not have CUDA. If you are not really interested in performing
simulations using GPU, you can set -DGMX_GPU=off during cmake
On Sat, Aug 24, 2013 at 12:15 PM, No One not1morepara...@yahoo.com wrote:
hi,
i'm having difficulties installing gromacs by creating static links to the
Hi,
I was wondering if there is a documentation of all the source code
variables is available or not.
--
gmx-users mailing listgmx-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
Hi,
Sorry to bother you again regarding this. But I am not sure, as to why
freeze + constraints should not work during a NPT simulation?
The update algorithm as shown in the manual does not say anything that
would fundamentally prevent this. In fact, one can use freezegroups +
constraints in
are not constrained,
things work fine.
I know this is a very round about way of getting things done, still i am
curious.
On Sep 10, 2013 4:12 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/10/13 2:59 PM, HANNIBAL LECTER wrote:
Hi,
Sorry to bother you again regarding this. But I am not sure, as to why
I am trying to simulate a peptide inside a nanotube and using isotropic
pressure coupling for the system. The nanotube is immersed in a cuboidal
box of water and aligned along the z direction of the box.
The XX, YY components of the stress tensor are about ~570 bars and the ZZ
component is about
500ps simulations. Yes everything is immersed in a bath of water. Can you
please elaborate a little more as to why do you doubt semiisotropic
coupling may not be necessary?
On Wed, Sep 11, 2013 at 9:05 AM, Justin Lemkul jalem...@vt.edu wrote:
On 9/11/13 9:01 AM, HANNIBAL LECTER wrote:
I am
Yes
On Wed, Sep 11, 2013 at 9:18 AM, Justin Lemkul jalem...@vt.edu wrote:
On 9/11/13 9:09 AM, HANNIBAL LECTER wrote:
500ps simulations. Yes everything is immersed in a bath of water. Can you
please elaborate a little more as to why do you doubt semiisotropic
coupling may not be necessary
Would there be artifacts because of that?
On Wed, Sep 11, 2013 at 9:20 AM, HANNIBAL LECTER hanniballecte...@gmail.com
wrote:
Yes
On Wed, Sep 11, 2013 at 9:18 AM, Justin Lemkul jalem...@vt.edu wrote:
On 9/11/13 9:09 AM, HANNIBAL LECTER wrote:
500ps simulations. Yes everything
Hi all,
I have been posting for a while with my problems in simulating peptides
inside CNTs. After a lot of trials it seems like simulating the CNT with
bonds and angles seems like a wise thing to do.
I am using the SD integrator + PR barostat. It seems like improper
thermostatting can blow up
for the parameters for CNT, if you need such...
Dr. Vitaly V. Chaban
On Fri, Sep 13, 2013 at 8:55 PM, HANNIBAL LECTER
hanniballecte...@gmail.com
wrote:
However, even if position restraints are not used, the error can be
reproduced. I am constraining the bonds in my CNTs though.
I
Is there a way to constraint bonds of a part of the system while keeping
the other part flexible? For example for a simulation with two proteins, I
would like to constraint the bonds of one and would like to keep the other
flexible.
I would prefer to use LINCS to constraint the system
--
. But still need to test a lot of things before I can decide on the
final settings.
On Tue, Sep 17, 2013 at 5:11 PM, HANNIBAL LECTER hanniballecte...@gmail.com
wrote:
Yes. That is the way to go about it. I was hoping for a more lazy
approach... Thanks anyways.
On Tue, Sep 17, 2013 at 5:07 PM
Yes. That is the way to go about it. I was hoping for a more lazy
approach... Thanks anyways.
On Tue, Sep 17, 2013 at 5:07 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/17/13 4:50 PM, HANNIBAL LECTER wrote:
Is there a smart way of writing the constraint sections in the topology
file other
/13 10:00 AM, HANNIBAL LECTER wrote:
Is there a way to constraint bonds of a part of the system while keeping
the other part flexible? For example for a simulation with two
proteins, I
would like to constraint the bonds of one and would like to keep the
other
flexible.
I would prefer
have parameters for CNTs such that they work with the SD
integrator with reasonable tau-t values?
On Tue, Sep 17, 2013 at 5:14 PM, HANNIBAL LECTER hanniballecte...@gmail.com
wrote:
@Vitaly. Yes you are right. However, I noticed that if I do not constraint
the bonds in my CNT my simulations run
Hi
I had tried using gromacs-4.6.1 to perform solute tempering. If you go
through terakawa's paper you have to describe the lambdas corresponding to
the temperatures. In your topology file define the params corresponding to
the two end states l=0 and l=1. Then define vdw, bonded and coulomb
31 matches
Mail list logo
