Dear Gromacs users,
I am doing SMD of a ligand pathway, and then want ot do the PMF analysis.
Initially I pulled the ligand from extra to intracellular side of the
protein. The pull code used are given below.
pull = umbrella
pull_geometry= distance
pull_dim
Hi,
This was a typo in configure.ac, the second line should say
--without-qmmm-orca.
Fixed it for the next release. Thanks for reporting.
Rossen
On 7/31/10 12:11 PM, Alan wrote:
For gmx 4.5 beta, I see with ./configure --help:
--without-qmmm-mopacUse modified Mopac 7 for QM-MM (see
Hi,
The tests haven't been ported to 4.5 yet but I hope to fix that before
the final release.
Rossen
On 7/31/10 7:08 PM, Alan wrote:
Is there a proper set of tests for gmx 4.5 because neither
ftp://ftp.gromacs.org/pub/tests/gmxtest-4.0.4.tgz or "git clone
git://git.gromacs.org/regressionte
From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Date: Wed, 4 Aug 2010 12:56:54 +1000
Subject: Re: [gmx-users] Precision in trajectory file
- Original Message -
From: Inon Sharony
Date: Tuesday, August 3, 2010 20:55
Subject: [gmx-users] Precision in trajectory file
To: "gmx-us
Jennifer Williams wrote:
Hi,
Is there some way of making the make_ndx file interactive so that I
can include it in a script?
I would usually type in "a C_O and O_C" to select my atoms
I've tried altering the example on the webpage for making commands
interactive:
make_ndx -flags <
try:
Aswathy wrote:
Dear Gromacs users,
I am doing SMD of a ligand pathway, and then want ot do the PMF
analysis. Initially I pulled the ligand from extra to intracellular side
of the protein. The pull code used are given below.
pull = umbrella
pull_geometry= dis
Hi Chris,
First of all, as Rossen said, the <=2.6.4 is a typo, it was meant to
be >=2.6.4, it _should_ work with 2.8.0 (I took the FindCUDA.cmake
script from the 2.8 cmake sources :), but...
icc is _not_ supported by CUDA, AFAIR some people reported getting it
work but only in some very limited
Hi Chris,
Though I'm repeating myself, for the sake of not leaving this post
unanaswered (btw reposts should be avoided as much as possible!):
First of all, as Rossen said, the <=2.6.4 is a typo, it was meant to
be >=2.6.4, it _should_ work with 2.8.0 (I took the FindCUDA.cmake
script from the 2.
Dear Szilárd and Rossen:
I have attempted with gcc4.4.0 and I got the same result. I can verify
that cmale/FindCUDA.cmake exists and contains the MARCO for
CUDA_INCLUDE_DIRECTORIES but it seems that this library is not, for
some reason, getting loaded in by at least
kernel/gmx_gpu_utils/C
I'm glad there's some interest in the test set. I'm happy to update what I did
for 4.0.7 for 4.5 also, but there are a number of issues that need attention
from someone other than me. I listed those that occurred to me here
http://lists.gromacs.org/pipermail/gmx-developers/2009-August/003586.htm
Hi guys,
>From what I've tested, it seems that performances decreases linearly with
the amount of tables used, exactly the opposite of what Lanyuan has said.
I've tested this for GROMACS 4.0.4 and from 1 to 190 tables. Near 190
tables, it seems that a threshold in performance starts to form, but n
Dear gmx users,
I want to calculate intermolecular RDF between N and carbonyl oxygen atoms
in a DPPC bilayer. As suggested in some mails in the mailing list i wanted
to generate one tpr file for the purpose containing exclusion 49 (as united
atom model of DPPC contains 50 atoms). But while generat
prithvi raj pandey wrote:
Dear gmx users,
I want to calculate intermolecular RDF between N and carbonyl oxygen
atoms in a DPPC bilayer. As suggested in some mails in the mailing list
i wanted to generate one tpr file for the purpose containing exclusion
49 (as united atom model of DPPC cont
Hi, All,
Does anyone know where the force field parameters for the heme in the
ff53a6 force field were obtained?
Much appreciated,
Art
Art Roberts
7254 Shoreline Dr. #130
San Diego, CA 92122
cell: 206-850-7468
email: aroberts99...@yahoo.com
skype=aroberts92122
--
gmx-users mailing list
It appears that the parameters in 53a6 are unchanged relative to 43a1, the
reference for which is the GROMOS manual. Unfortunately, you have to pay the
licensing fee to obtain the manual. There are certainly several literature
references for various aspects of the GROMOS functional form and
You've basically got the idea. As a subtle point, the "strength" of a method is
completely user-defined (by the tau_p parameter, how frequently the temperature
is coupled). No one method is "stronger" than another, but it is correct to say
that the Nose-Hoover thermostat produces a rigorous
Hello
I am trying to constraints of a bond. I checked the distance using g_dist,
distance changes from 3.5 A to ~ 8.0A.
Can anyone tell why it changes.
Here I have pasted mdp file and itp file.
Nilesh
Solvent.itp
; Derived from parsing of runfiles/alat.top.orig
[ defaults ]
; nbfunccomb-rul
Nilesh Dhumal wrote:
Hello
I am trying to constraints of a bond. I checked the distance using g_dist,
distance changes from 3.5 A to ~ 8.0A.
Can anyone tell why it changes.
Here I have pasted mdp file and itp file.
Maybe there's a bug in the interpretation of the constraints? The combination
constraints = all-bonds is working. I have solvent molecule for which I
don't want constraints on them. I can't use constraints = all-bonds for
simulation.
Nilesh
On Wed, August 4, 2010 9:48 pm, Justin A. Lemkul wrote:
>
>
> Nilesh Dhumal wrote:
>
>> Hello
>> I am trying to constraints of a bond.
Nilesh Dhumal wrote:
constraints = all-bonds is working. I have solvent molecule for which I
don't want constraints on them. I can't use constraints = all-bonds for
simulation.
So you used g_dist to determine the distances with the setup shown below, but
did you correct for PBC effects? Is
Its oscillate between +/- 3-4 A.
If I freeze the distance by using freeze groups and dim in mdp file. It
works perfectly for NVT simulations. It oscillate for NPT simulation.
Nilesh
On Wed, August 4, 2010 9:56 pm, Justin A. Lemkul wrote:
>
>
> Nilesh Dhumal wrote:
>
>> constraints = all-bonds is
Nilesh Dhumal wrote:
Its oscillate between +/- 3-4 A.
If I freeze the distance by using freeze groups and dim in mdp file. It
works perfectly for NVT simulations. It oscillate for NPT simulation.
I don't know if there have been any changes (I don't see anything in the
revision history), but
Then it looks there is bug ater define the constraints in itp file, bond
distance changes.
On Wed, August 4, 2010 10:22 pm, Justin A. Lemkul wrote:
>
>
> Nilesh Dhumal wrote:
>
>> Its oscillate between +/- 3-4 A.
>> If I freeze the distance by using freeze groups and dim in mdp file. It
>> works
Nilesh Dhumal wrote:
Then it looks there is bug ater define the constraints in itp file, bond
distance changes.
Then file a bugzilla so the developers can either confirm the bug and fix it, or
provide an explanation as to what is going on.
-Justin
On Wed, August 4, 2010 10:22 pm, Justi
On Wed, Aug 4, 2010 at 4:31 PM, Justin A. Lemkul wrote:
>
>
> Aswathy wrote:
>
>> Dear Gromacs users,
>>
>> I am doing SMD of a ligand pathway, and then want ot do the PMF analysis.
>> Initially I pulled the ligand from extra to intracellular side of the
>> protein. The pull code used are given b
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