Dear,
Thanks a lot for your suggestion Justin.
I have a box 3 3 20 and want to plot the temperature along the z axis. I
did the commands:
g_energy -f NVT_20ns.edr -s topol.top -o temp
g_analyze -f temp.xvg -dist temp.xvg
and got the results:
281.9 0 282 0.000149997 282.1 0 282.2 0 282.3 0
On 11/19/12 10:04 PM, André Farias de Moura wrote:
from the statistical thermodynamics standpoint, rdf must be the same for
both choices of reference group, i.e.,solute-solvent and solvent-solute
must yield exactly the same rdf, the only difference being expected for the
cumulative numbers, whi
from the statistical thermodynamics standpoint, rdf must be the same for
both choices of reference group, i.e.,solute-solvent and solvent-solute
must yield exactly the same rdf, the only difference being expected for the
cumulative numbers, which depend on the particles number density. The
reason w
On 11/19/12 12:09 PM, Parisa Rahmani wrote:
Dear gmx users
I have a problem with running parallel jobs on my Debian system(Openmpi
installed on it),
**Linux debian 3.2.0-1-amd64 #1 SMP , UTC 2012 x86_64 GNU/Linux**
I am using gmx 3.3.3, because of the *lambda dynamics* method which is
implemen
On 11/19/12 11:50 AM, shch406 wrote:
I would have chosen the groups in the opposite manner. You're interested in
the
presence of water around the chosen arginine residue, not the presence of
arginine around water, right? Given this order of chosen groups, the RDF
seems
to make sense (very
Xavier is right, except that you can also reduce the size of your system. You
can take larger steps in temperature
if you have fewer atoms. If you are using a cubic system, you can move to a
rhombic dodecahedron.
Even constraining all bonds will help a bit here (vs. harmonic bonds).
There are
On 11/19/12 2:44 PM, Oliver Mirus wrote:
Hi,
I've downloaded Gromacs 4.6:
git checkout --track -b release-4-6 origin/release-4-6
With '-msse4.1' added to CMAKE_C_FLAGS it finally compiled.
But a test run with 1 CPU & 1 GPU failed with the following message
before it started :
--
Hi,
I've downloaded Gromacs 4.6:
git checkout --track -b release-4-6 origin/release-4-6
With '-msse4.1' added to CMAKE_C_FLAGS it finally compiled.
But a test run with 1 CPU & 1 GPU failed with the following message
before it started :
--
mdrun -deffnm gputest -gpu_id $g
Hi Stephane,
The confusion was my fault, I did not realise that there were newly
developed CHARMM36 protein parameters (Justin kindly pointed this out).
You were quite correct that the contribution only contains the update
for the lipids.
Cheers
Tom
On 19/11/12 18:49, ABEL Stephane 175950
Hi Thomas and Justin,
I agree with you, but I think that Albert asked if the GROMACS 4.5.4 version of
the CHARMM36 force field files contain the newly developed parameters for
protein (also called CHARMM36) and described in
Best, R. B., Zhu, X., Shim, J., Lopes, P. E. M., Mittal, J., Feig, M
On 11/19/2012 05:48 PM, Thomas Piggot wrote:
I must have missed that one, thanks for the link!
So, to confirm, the protein force field in the CHARMM36 force field
contribution is the CHARMM22 protein force field with the CMAP
correction. The contribution is just for the updated CHARMM36 lipids
On Mon, Nov 19, 2012 at 4:09 PM, Thomas Evangelidis wrote:
> Hi Szilárd,
>
> I compiled with the Intel compilers, not gcc. In case I am missing
> something, these are the versions I have:
>
Indeed, I see it now in the log file. Let me try with icc 13 and will get
back to you.
>
> glibc.i686
Well either you use more replicas or you reduce the temperature
range ...
There is no way around!
On Nov 19, 2012, at 5:54 PM, Kenny Bravo Rodriguez wrote:
Dear All,
i am trying to performed REMD simulations using Gromacs.
My question is concerning the temperature distribution and the
nu
Dear All,
i am trying to performed REMD simulations using Gromacs.
My question is concerning the temperature distribution and the number of
replica.
I need to run 24 replicas of my system with a temperature range of
290-400 K. How can I select the temperatures values for each replica?
I tried t
>I would have chosen the groups in the opposite manner. You're interested in
the
>presence of water around the chosen arginine residue, not the presence of
>arginine around water, right? Given this order of chosen groups, the RDF
seems
>to make sense (very low probability that arginine is clos
I must have missed that one, thanks for the link!
So, to confirm, the protein force field in the CHARMM36 force field
contribution is the CHARMM22 protein force field with the CMAP
correction. The contribution is just for the updated CHARMM36 lipids.
Cheers
Tom
Justin Lemkul wrote:
On 11
On 11/19/12 11:28 AM, Thomas Piggot wrote:
Hi,
As I understand it, the current and most up to date CHARMM protein force field
(as included in both the charmm27 and charmm36 force field directories) is the
CHARMM22 protein force field with the CMAP correction. In other words there
would be no d
Hi,
As I understand it, the current and most up to date CHARMM protein force
field (as included in both the charmm27 and charmm36 force field
directories) is the CHARMM22 protein force field with the CMAP
correction. In other words there would be no difference between the two
options original
Hello
I would like to perform a molecular simulation with the AMBER99SB FF ,
tip3p water model and reaction field for long range interactions. Which
value of epsilon_rf (The relative dielectric constant of the reaction
field) do I have to use?
Thanks
Williams
--
gmx-users mailing listgmx-us
Hi,
Probably the "CHARMM27_protein+Charmm36_lipids" version. AFAIK, the second
version was not already converted in GROMACS format.
Stephane
---
hello:
I found a charmm36.tar.gz in Gromacs website
GROMACS 4.5.4 version of the CHARMM36 fo
On 11/19/12 10:54 AM, Bahar Mehrpuyan wrote:
thanks Justin for the reply
sorry , I asked my question in a wrong way,
I mean should I do geometry optimization for that capped peptide(protein)?(with
mm force field and steepest descent algorithm)
You should do an energy minimization with whatev
thanks Justin for the reply
sorry , I asked my question in a wrong way,
I mean should I do geometry optimization for that capped peptide(protein)?(with
mm force field and steepest descent algorithm)
From: Justin Lemkul
To: Bahar Mehrpuyan ; Discussion list fo
On 11/19/12 5:30 AM, Bahar Mehrpuyan wrote:
Hi gmx users
I want to cap my peptide (adding ACE & NAC) with Avogadro package , my question
is , should I minimize the capped peptide with forcefields(molecular mechanics)
available in avogadro, then use it in the simulation? or just simulation pr
Hi Szilárd,
I compiled with the Intel compilers, not gcc. In case I am missing
something, these are the versions I have:
glibc.i6862.15-57.fc17
@updates
glibc.x86_64 2.15-57.fc17
@updates
glibc-common.x86_64 2.15-57.fc17
@upda
Thomas & Albert,
We are unable to reproduce the issue on FC 17 with glibc 2.15-58 and gcc
4.7.2.
Please try to update your packages (you should have updates available for
glibc), try recompiling with the latest 4.6 code and report back whether
you succeed.
Cheers,
--
Szilárd
On Fri, Nov 16, 2
hello:
I found a charmm36.tar.gz in Gromacs website
GROMACS 4.5.4 version of the CHARMM36 force field files. These updated
CHARMM lipids allow the all-atom simulations of membrane and
membrane-protein systems without the use of surface tension. Check out
the forcefield.doc for more informa
Hi gmx users
I want to cap my peptide (adding ACE & NAC) with Avogadro package , my question
is , should I minimize the capped peptide with forcefields(molecular mechanics)
available in avogadro, then use it in the simulation? or just simulation
procedures (minimization and equilibration) is su
On 2012-11-19 10:42, Albert wrote:
On 11/19/2012 10:27 AM, David van der Spoel wrote:
On 2012-11-19 09:57, Albert wrote:
hello:
I've got a K+ near an Asp residue. I found that If I include the K+
in H++ calculation, the Asp is deprotonated while it is protonated if I
didn't include it. I am
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trjconv
19 nov 2012 kl. 10.47 skrev Shima Arasteh:
> Dear gmx users,
>
> Is there any command in GROMACS, which I can use it to save frames of
> trajectory file in pdb format?
>
>
>
> Sincerely,
> Shima
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailma
Dear gmx users,
Is there any command in GROMACS, which I can use it to save frames of
trajectory file in pdb format?
Sincerely,
Shima
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/S
On 11/19/2012 10:27 AM, David van der Spoel wrote:
On 2012-11-19 09:57, Albert wrote:
hello:
I've got a K+ near an Asp residue. I found that If I include the K+
in H++ calculation, the Asp is deprotonated while it is protonated if I
didn't include it. I am quite confused for this. I am just
On 2012-11-19 09:57, Albert wrote:
hello:
I've got a K+ near an Asp residue. I found that If I include the K+
in H++ calculation, the Asp is deprotonated while it is protonated if I
didn't include it. I am quite confused for this. I am just wondering
will the g_protonate will solve this probl
hello:
I've got a K+ near an Asp residue. I found that If I include the K+
in H++ calculation, the Asp is deprotonated while it is protonated if I
didn't include it. I am quite confused for this. I am just wondering
will the g_protonate will solve this problem?
thank you very much.
best
Al
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