On 2011-5-14 0:52, zw...@cam.ac.uk wrote:
Hello.
I am writing to ask if current GROMACS-GPU supports CMAP dihedrals in
CHARMM.
We are trying to run GROMACS on GPU. It is mentioned on GROMACS
website
(http://www.gromacs.org/Downloads/Installation_Instructions/GPUs?highlight=gpu)
that CMAP d
Hi,
Only OpenMM-2.0 (no CMAP) is supported in the gromacs 4.5 releases.
There are no plans at the moment to support all new functionality in
OpenMM-3.0.
Cheers,
Rossen
On 5/16/11 9:06 AM, Zhi Wang wrote:
On 2011-5-14 0:52, zw...@cam.ac.uk wrote:
Hello.
I am writing to ask if current GROMA
Dear gmx-users,
first let me resume my attempts on this question.
1) Using:
pdb2gmx -f my_protein.pdb -o my_protein.gro -p my_protein.top
I obtained a .gro file in which the numbering of each chain correctly
starts from 21 to 379 in both chains, but no chain ID is present, so I
cannot distinguish
Hello users,
Can anyone tell how to calculate the normal-normal angle between two
stacking tyrosine residues as a function of time.
--
---
Regards,
Bipin Singh
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Please searc
To all gromacs user,
I m trying the KALP15 in water tutorial, in which at the second command "grompp
-f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr", i have got the
following error:
ERROR 1 [file dppc.itp, line 112]:
No default LJ-14 types
ERROR 2 [file dppc.itp, line 113]:
No def
Dear All,
Hi! I 'm using Charmm-gui to generate an empty membrane pdb and toppar, i
managed to get the charmm topology from toppar directory. With that, I'm
trying to put additional lipid topology from charmm-gui into
/charmm27.ff/lipids.rtp (gromacs4.5.4) for my empty membrane. But with
pdb2gmx,
vidhya sankar wrote:
Dear justin,
Thank you for your reply,
can i
use pull code of umberla pullings
in Protein ligand interaction.
otherwise is it possible to use pull code for chain pulling ?.
Y
Preeti Gupta wrote:
To all gromacs user,
I m trying the KALP15 in water tutorial, in which at the second command
"grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr", i have
got the following error:
ERROR 1 [file dppc.itp, line 112]:
No default LJ-14 types
You haven't prop
Bing Bing wrote:
Dear All,
Hi! I 'm using Charmm-gui to generate an empty membrane pdb and toppar,
i managed to get the charmm topology from toppar directory. With that,
I'm trying to put additional lipid topology from charmm-gui into
/charmm27.ff/lipids.rtp (gromacs4.5.4) for my empty memb
Hi All,
Sorry to bug you all about this - it's been mentioned a few times but I can't
find an answer that seems to relate to the situation I've got.
I'm trying to use the g_fdaconv / g_fdatools within gromacs 4.0.5, however,
everytime I type the commands I get 'g_fda*: command not found'.
The
Natalie Stephenson wrote:
Hi All,
Sorry to bug you all about this - it's been mentioned a few times but I
can't find an answer that seems to relate to the situation I've got.
I'm trying to use the g_fdaconv / g_fdatools within gromacs 4.0.5,
however, everytime I type the commands I get 'g
Anna Marabotti wrote:
Dear gmx-users,
first let me resume my attempts on this question.
1) Using:
pdb2gmx -f my_protein.pdb -o my_protein.gro -p my_protein.top
I obtained a .gro file in which the numbering of each chain correctly
starts from 21 to 379 in both chains, but no chain ID is presen
Sorry for the confusion - didn't mean I'd used a wildcard when typing the
commands ... just meant I get that response for both commands.
They're an add on created from a the Molecular BioMechanics group
(http://projects.eml.org/mbm/website/fda_gromacs.htm) - I've downloaded they're
software as
Natalie Stephenson wrote:
Sorry for the confusion - didn't mean I'd used a wildcard when typing the
commands ... just meant I get that response for both commands.
They're an add on created from a the Molecular BioMechanics group
(http://projects.eml.org/mbm/website/fda_gromacs.htm) - I've down
Hi Natalie,
You're in the wrong place, and probably trying the wrong thing. The
FDAtools are not part of Gromacs and if you encounter issues with them
you should raise it with the authors. They may have a user list too.
Aside from that, the FDAtools seem to be an R package. That means that
they w
Thanks loads ... that worked perfectly!! Environment configured!! :D
xxx
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: 16 May 2011 16:09
To: Discussion list for GROMACS users
Subje
Hello,
the g_energy tool in Gromacs 4.0.7 provides calculation of viscosity (-vis) and
surface tension (-o surften):
a) Both, the shear and bulk viscosity are calculated with -vis tool. What are
the equations for calculating them? In the manual, there is only the equation
for the shear viscosi
Hi Gmxers,
I am wondering if NMA has been introduced into QMMM part of gromacs.
I am trying to get vibrational frequencies of proteins by normal mode analysis
(NMA) in the framework of QMMM.
Thanks,
Yao
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Hello,
I want to compile the source code gmx_hbond.c after the below
mentioned bugfix, I have already installed gromacs 4.5.3, how can I
compile only gmx_hbond.c in already installed
gromacs 4.5.3.
>Hi,
>There have been reports about inconsistencies between older (<= 4.0.7?) and
>newer versio
On 17/05/2011 3:40 PM, bipin singh wrote:
Hello,
I want to compile the source code gmx_hbond.c after the below
mentioned bugfix, I have already installed gromacs 4.5.3, how can I
compile only gmx_hbond.c in already installed
gromacs 4.5.3.
If you've built using configure, then there is no way
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