Hi everyone!
I am currently studying CHARMM ff and I have a question on the functional type
of the CHARMM dihedral. On the ffbonded.itp, the function type for CHARMM
dihedrals is 9. However, this functional type is not listed on Table 5.5 of the
manual. I read that there are 9 supported
On 10/04/2011 4:12 PM, Mr Bernard Ramos wrote:
Hi everyone!
I am currently studying CHARMM ff and I have a question on the
functional type of the CHARMM dihedral. On the ffbonded.itp, the
function type for CHARMM dihedrals is 9. However, this functional type
is not listed on Table 5.5 of the
Dear All
I used the following commands accoring to Extending Simulation in
gromacs/Documentation/how-tos/Extending Simulation
to extend my simulation.
I entered:
tpbconv -s npt-1.tpr-extend 100 -o npt-1-extend.tpr
nohup mpirun -np 4 mdrun -s npt-1-extend.tpr -cpi npt-1.cpt
Ii run
On 10/04/2011 5:40 PM, mohsen ramezanpour wrote:
Dear All
I used the following commands accoring to Extending Simulation in
gromacs/Documentation/how-tos/Extending Simulation
to extend my simulation.
I entered:
tpbconv -s npt-1.tpr-extend 100 -o npt-1-extend.tpr
nohup mpirun -np 4
Dear Dr.Justin
As you have noticed in your tutorials,It is better to use Nose-Hoover for
tempreture in the NPT.mdp file.
You have used tau-t = 0.1 in most of your md.mdp files for generating npt
ensemble.
When I use a npt file with these settings,there is a Note as following:
sorry,i can't
Dear Dr.Mark
On Sun, Apr 10, 2011 at 12:20 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 10/04/2011 5:40 PM, mohsen ramezanpour wrote:
Dear All
I used the following commands accoring to Extending Simulation in
gromacs/Documentation/how-tos/Extending Simulation
to extend my simulation.
On 10/04/2011 6:04 PM, mohsen ramezanpour wrote:
Dear Dr.Mark
On Sun, Apr 10, 2011 at 12:20 PM, Mark Abraham
mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote:
On 10/04/2011 5:40 PM, mohsen ramezanpour wrote:
Dear All
I used the following commands accoring to
Dear Dr.Mark
Thank you very much
you are right
I understood your mean exactly,
On Sun, Apr 10, 2011 at 12:44 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 10/04/2011 6:04 PM, mohsen ramezanpour wrote:
Dear Dr.Mark
On Sun, Apr 10, 2011 at 12:20 PM, Mark Abraham
Dear All
How can I determine the converged value of a simulation?
Because the pressure has big oscilations around it's converging value but it
is difficult to determine that value.
can everybody guide me?
Thanks in advance
--
gmx-users mailing listgmx-users@gromacs.org
Thank you David,
My micelle simulated with the GROMOS ff slightly differs (size and shape)
from the two others micelles, so i expected that the values total SAS value
slightly differ. In case of the headgroup, they are located in the micelle
interface region, so the SAS in case of the micelle
On 2011-04-10 11.11, sa wrote:
Thank you David,
My micelle simulated with the GROMOS ff slightly differs (size and
shape) from the two others micelles, so i expected that the values total
SAS value slightly differ. In case of the headgroup, they are located in
the micelle interface region, so
He told me you can use up to 0.5 in an off-list email and in fact, does so
in the KALP-15 in DPPC example...
On 2011-04-10 02:54:15AM -0500, mohsen ramezanpour wrote:
Dear Dr.Justin
As you have noticed in your tutorials,It is better to use Nose-Hoover for
tempreture in the NPT.mdp file.
On 10/04/2011 6:48 PM, mohsen ramezanpour wrote:
Dear All
How can I determine the converged value of a simulation?
Because the pressure has big oscilations around it's converging value
but it is difficult to determine that value.
Longer simulations on bigger systems.
Mark
--
gmx-users
majid hasan wrote:
Sorry, the pdb file is bigger than 50k so it won't attach, so its pasted
below. Output of pdb2gmx is attached.
You have numerous problems with this .pdb file:
1. All residues are listed as being the 3' end form. Your chain should start
with a 5' end, include the
Dear GMX users,
I have a question about running MD simulation using amber force field. It is
easy to prepare the top and gro files of protein with amber force field, but
how should I prepare the itp and gro files of small molecules with GAFF force
field? I know the program ANTECHAMBER and
fancy2012 wrote:
Dear GMX users,
I have a question about running MD simulation using amber force
field. It is easy to prepare the top and gro files of protein with amber
force field, but how should I prepare the itp and gro files of small
molecules with GAFF force field? I know the
Dear Dr.Mark
thank you for your attention
How long is enough?
for example I have run 200 ps for making npt(p=1 bar) for my system (300
nm^3)
But the pressure is oscilating so much,and I can't be sure if it has
converged or not!
of course its average is approximately 5 bar (at the end of log file)
On 10/04/2011 9:41 PM, mohsen ramezanpour wrote:
Dear Dr.Mark
thank you for your attention
How long is enough?
For example, when the size of error estimate reported by g_energy is
smaller than the quantity you are trying to observe. That might take
many nanoseconds in the case of
2011/4/10 Mark Abraham mark.abra...@anu.edu.au:
On 10/04/2011 11:44 AM, Justin A. Lemkul wrote:
Maybe this is unrelated to the underlying problem, but hopefully it helps
in the long run. Nothing worse than a reviewer saying, Nice project, but
100% of the data are junk.
Bad idea, and 100%
2011/4/10 Mark Abraham mark.abra...@anu.edu.au:
On 10/04/2011 10:58 AM, devicerandom wrote:
A polite request for correct behaviour is suitable. Use of ALL CAPS is also
a breach of netiquette. :-)
Ouch. I just wanted to convey strength, it's not like I WROTE ALL THE
MAIL IN ALL CAPS :-)
You need to look at the dependence of the statistical value (in this
case the average pressure) with (a) increasing equilibration time that
you discard prior to collecting pressure data, and (b) increasing
production simulation time that you include in your average.
Create the first plot,
very much in advance!
--
Best wishes,
Qinghua Liao
Ph.D student of Tianjin University, China
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Okay, thank you. I'll try to fix it.
Majid
From: Justin A. Lemkul jalem...@vt.edu
To: Gromacs Users' List gmx-users@gromacs.org
Sent: Sun, April 10, 2011 4:17:59 AM
Subject: Re: [gmx-users] Dangling bond error for dna
majid hasan wrote:
Sorry, the pdb file
Thank you David
A bientôt
SA
--
Message: 1
Date: Sun, 10 Apr 2011 11:17:15 +0200
From: David van der Spoel sp...@xray.bmc.uu.se
Subject: Re: [gmx-users] Different g_sas values between AMBER, CHARMM
and
Is there any software that generates .pdb file consistent with amber forcefield
requirements? I tried 3DNA, and GABEDIT, but 3DNA doesn't name residues in
correct format i.e DX, and gabedit names every residue as DX3.
Thanks,
Majid
From: Justin A. Lemkul
Okay, I am trying AmberTools as well. Thanks Justin!
Majid
From: Justin A. Lemkul jalem...@vt.edu
To: Gromacs Users' List gmx-users@gromacs.org
Sent: Sun, April 10, 2011 10:16:57 AM
Subject: Re: [gmx-users] Dangling bond error for dna
majid hasan wrote:
Is
Dear gmxers,
I have had tried to install gmx-4.5.4 by compiling the source code. The
first step ./configure finished without any error, but the second step running
make reported some errors as follows
/usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../x86_64-suse-linux/bin/ld:
Dear gmxers,
I have had tried to install gmx-4.5.4 by compiling the source code.
The first step ./configure finished without any error, but the second
step running make reported some errors as follows
/usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../x86_64-suse-linux/bin/ld:
Hello gmx users,
My system for NVT equilbration runs into segmentation fault as soon as I try
to run it.
It does not give any warning or hint of what might be going wrong.
Since I am a new user I am having difficulty exploring the plausible
reasons.
System: Protein( polyhistidine), 20
Should I couple a ligand associated with a membrane protein to the same
COM group as the Protein_POPC group? It makes sense to me that would be the
case since if we are investigating the interaction between protein+membrane
and ligand we want to have the same COM correction vector applied to
Hello gmx users,
My system for NVT equilbration runs into segmentation fault as soon as
I try to run it.
It does not give any warning or hint of what might be going wrong.
Since I am a new user I am having difficulty exploring the plausible
reasons.
System: Protein( polyhistidine), 20
Hi everyone!
The OPLS AA SEI for carbohydrates scales the 1,5 and 1,6 interaction
by a certain factor. How do I go about introducing the scaling of
these intearctions in the ff parameters? The CHARMM ff also has
certain 1,4 parameters, I am not sure how we can go about placing
these specific
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