I would couple it with the membrane to be honest. The point of the different
groups is to avoid the hot solvent cold solute sitution. Molecules with
similar degrees of freedom have comparable heat capacities. Your small
peptide is closer in size and bond layout to a lipid chain than to water.
The
Hi
I have a system with a lipid bilayer (128 phospolipids), aproximately 30 SOL
molecules per lipid, and a small highly charged peptide at certain distance
from the bilayer. I want to do a pulling simulation in order to pull the
peptide inside the membrane along the z-direction. So, taking into ac
What do you mean spurious protein movement?
Also, the instantaneous electrostatic potential is always uneven, and I am not
sure why the average
electrostatic potential would change with excess salt, excepting that I would
expect it to converge more rapidly with excess salt.
Finally, if you are
Thanks Chris, very good points. I would like to add a potential drawback
for not using salt taken from my experience:
I simulated a coiled coil with one end having charge +12 and the other
zero. I ran a simulation with just 12 Cl- counter ions which tended to
cluster near the positively charged ta
Hi Mikhail,
I am using GMX4.5.5 to simulate SWM4-NDP polarizable water model, it
is working fine.
When i am running separately NA+ polarizable ion in SWM4-NDP water
and Cl- polarizable ion in SWM4-NDP polarizable water model, it is
working fine.
But when I use the both NA+ and CL- (NaCl salt solut
There are 4 reasons that I can think of:
A) Didn't consider it or know how to do it
B) Repeating a previous simulation (possibly with some modifications) -- e.g.
simulation a protein in a lipid bilayer
using lipid parameters that have been shown to give the desired area per lipid
in the absence
On 10/11/12 10:54 AM, R.Vidya Rajendran (10PHD013) wrote:
Hello Justin,
With regards to my second query ...to suppress the size of .trr I can
set nstxout, nstvout, and nstfout to zero in the .mdp file, But I am
afraid It will affect the .xtc file too.
It will not. The frames in the .xtc fi
Hello Justin,
With regards to my second query ...to suppress the size of .trr I can
set nstxout, nstvout, and nstfout to zero in the .mdp file, But I am
afraid It will affect the .xtc file too.
regards
Vidya
On Thu, Oct 11, 2012 at 5:24 PM, Justin Lemkul wrote:
>
>
> On 10/11/12 10:17 AM, R.Vid
On 10/11/12 10:27 AM, Shine A wrote:
Sir,
I am studying the dynamics of membrane proteins using KALP-15 in DPPC.
But during minimization getting error like this..
There is no domain decomposition for 4 nodes that is compatible with
the given box and a minimum cell size of 18.5346 nm
Please keep the discussion on the mailing list. I have told you several times
that I do not reply to private Gromacs help requests unless I ask you to send me
files for diagnostic purposes. You stand a better chance of resolving the issue
with the help of the community, and the resolution wi
On 11 okt 2012, at 16.17, R.Vidya Rajendran (10PHD013) wrote:
> Hello Friends,
>
> I have two very specific queries regarding gromacs output files.
>
> 1) Since we can generate .xtc file during mdrun, Is is possible to
> stop generating .trr files, because it used to be very huge and less
> use
Sir,
I am studying the dynamics of membrane proteins using KALP-15 in DPPC.
But during minimization getting error like this..
There is no domain decomposition for 4 nodes that is compatible with
the given box and a minimum cell size of 18.5346 nm
Change the number of nodes or mdrun opti
On 10/11/12 10:17 AM, R.Vidya Rajendran (10PHD013) wrote:
Hello Friends,
I have two very specific queries regarding gromacs output files.
1) Since we can generate .xtc file during mdrun, Is is possible to
stop generating .trr files, because it used to be very huge and less
useful.
Set nstx
Hello Friends,
I have two very specific queries regarding gromacs output files.
1) Since we can generate .xtc file during mdrun, Is is possible to
stop generating .trr files, because it used to be very huge and less
useful.
2) .xtc & .tpr files generated by gms4.5.5 version is not readable by
gm
Hi,
You don't have to replace existing installations. You can simply build a new
gromacs version and install it in a different folder than your existing
installation. If you still want only the g_select tool for whatever reason you
can usually chose to only build one tool (and its dependencies)
Dear Gromacs Guru's,
I currently have an old installation of gromacs (4.0.7) on my cluster and
the newer 4.5.4 on a gpu-machine that my group was using to explore the
gromacs-gpu acceleration. While using the newer version we found that
g_select was incredibly useful and seemed to work with both o
On 10/11/12 9:33 AM, Venkat Reddy wrote:
Thanks Justin for the information. By the way, Could you please give me a
hint on the release of new GPU-version (4.6)?
As I posted yesterday, I do not have any insight on a specific release date.
It's close, but I'm not involved in any of the remain
Thanks Justin for the information. By the way, Could you please give me a
hint on the release of new GPU-version (4.6)?
On Thu, Oct 11, 2012 at 4:20 PM, Justin Lemkul wrote:
>
>
> On 10/10/12 11:53 PM, Venkat Reddy wrote:
>
>> Dear all,
>> I am doing a protein-ligand simulation and following Jus
ps: There is a fix for this issue in Gerrit code review:
https://gerrit.gromacs.org/#/c/1175/
which introduces a fix genbox -allpair. This avoid the memory-leaky
neighbor searching, which is the reason for your problem.
Jochen
Am 10/11/12 10:56 AM, schrieb Jochen Hub:
Hi,
this is due to t
Thanks.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Discussion list for GROMACS users
Cc:
Sent: Thursday, October 11, 2012 3:00 PM
Subject: Re: [gmx-users] Secondary structure after InflateGRO step - protein in
lipid membrane
On 10/11/12 7:27 AM, Shima Arasteh w
On 10/11/12 7:27 AM, Shima Arasteh wrote:
This is a sample of energy minimization, solvation and ion neutralization in my
own system ( protein in POPC):
Steepest Descents converged to Fmax < 100 in 18240 steps
Potential Energy = -1.0357691e+06
Maximum force = 8.0741402e+01 on atom 4716
This is a sample of energy minimization, solvation and ion neutralization in my
own system ( protein in POPC):
Steepest Descents converged to Fmax < 100 in 18240 steps
Potential Energy = -1.0357691e+06
Maximum force = 8.0741402e+01 on atom 4716
Norm of force = 3.1694601e+00
I think it
On 10/11/12 5:57 AM, Shima Arasteh wrote:
I visualized the last output mdrun of KALP15-DPPC simulation, the secondary
structure of protein is complete and it seems OK. Can I trust on it and not
care about the visualization of system after inflategro?
That's probably a reasonable conclusio
On 10/10/12 11:53 PM, Venkat Reddy wrote:
Dear all,
I am doing a protein-ligand simulation and following Justin's tutorials. I
have confusion in passing check point file to the next step in position
restrain simulation (during NPT). I am slowly releasing the restraints
during NPT simulation, *v
On 10/10/12 11:27 PM, Elie M wrote:
Understandable. I meant the content of the .n2t file itself ; will it contain
the same info as the OPLSAA with just changes in values according to the CHARMM
field?
Yes. File formats are always the same.
-Justin
Thank you
Elie
Date: Wed, 10 Oct 201
I visualized the last output mdrun of KALP15-DPPC simulation, the secondary
structure of protein is complete and it seems OK. Can I trust on it and not
care about the visualization of system after inflategro?
Sincerely,
Shima
- Original Message -
From: Shima Arasteh
To: Discussio
Thanks for your explanation.
I'm doing protein insertion in lipid-membrane following Justin's tutorial
steps, but My Protein and Lipid Membrane are different of KALP15 and DPPC.
Now, when I visualized .gro file of last iteration in KALP15-DPPC ( the
simulation what I did sometime ago to lear
Hi,
this is due to the way genbox -ci is currently implemented. It calles
add_conf() too often which leaks memory. So you'll have to edit the code.
Jochen
You'll have to edit the genbox code in order
Am 10/10/12 7:14 PM, schrieb Dr. Vitaly Chaban:
Thanks..You are right...The last line of
See the SHAKE algorithm in the manual.
Especially equation (3.98)
-> G_i = \sum_k \lambda_k * (\partial \sigma_k)/(\partial r_i)
where G_i is the constraint force
\sigma_k are the equations for the constraints
and \lambda_k is the lagrange multiplier
'Understanding molecular simulation' (D. Frenk
On Thu, Oct 11, 2012 at 12:19 AM, Juliette N. wrote:
> Hi,
>
> I will try to compress before doing genbox. As for the number of atoms, as I
> said I dont intend to fill up the whole box with solvent.
If you do not fill the whole box, it would be probably essentially the
same as if you have no s
30 matches
Mail list logo
