On 27/01/2012 6:22 PM, Antila Hanne wrote:
Dear experts,
I'm a bit confused about the use wildcards in the dihedral definitions
of .itp force field files. I'm under the impression that explicit
definition of a dihedral (e.g. OS-CT-CT-OS) is always used if
available and it overwrites any
On 27/01/2012 8:59 PM, Mark Abraham wrote:
On 27/01/2012 6:22 PM, Antila Hanne wrote:
Dear experts,
I'm a bit confused about the use wildcards in the dihedral definitions
of .itp force field files. I'm under the impression that explicit
definition of a dihedral (e.g. OS-CT-CT-OS) is always
The following is a part of the dna pdb file, which I am using:
ATOM 1 OH DG5 X 1 13.663 36.760 21.465 0.00 0.00
ATOM 2 CT DG5 X 1 14.791 36.040 21.150 0.00 0.00
ATOM 3 CT DG5 X 1 14.771 34.703 21.873 0.00 0.00
ATOM 4 OS DG5 X 1
Hello,
Am anik. Am using gromacs 4.5.5
I could not find the proper reason of the foillowig failure of my job. please
help.
The following is a part of the dna pdb file, which I am using:
ATOM 1 OH DG5 X 1 13.663 36.760 21.465 0.00 0.00
ATOM 2 CT DG5 X 1
I know that this topic has been mentioned again in the mailing list, yet no
explicit answer has been given. So my questions are:
1. How can I utilize the output files of g_cluster (rms-distribution.xvg,
cluster-sizes.xvg, cluster-id-over-time.xvg, cluster-transitions* ) to
decide which is the
On 27/01/2012 9:50 PM, Anik Sen wrote:
Hello,
Am anik. Am using gromacs 4.5.5
I could not find the proper reason of the foillowig failure of my job.
please help.
The following is a part of the dna pdb file, which I am using:
ATOM 1 OH DG5 X 1 13.663 36.760 21.465
Hi!
I posted a message before regarding the reverse transformation with g_fg2cg
command. Now I have managed to re-numerate correctly the residues so that
it doesn't complain about it but I have come across a different problem.
when I run the command it doesn't recognize the ions NA+. So I was
On 28/01/2012 12:54 AM, shahid nayeem wrote:
Dear All
I have done MMPBSA calculation on some complexes. It calculates
energy in terms of polar contribution to solvation as PBSUR and
nonpolar contribution to solvation as PBCAL and sum of these two terms
as PBSOL. It appears to me that PBSOL
Hi all,
I have two files (Topology and Parameter files) in NAMD format (*.inp). I
am going to use them in GROMACS.
Can you help me how can I use them?
Kind Regards,
Dariush Mohammadyani
Department of Structural Biology
University of Pittsburgh School of Medicine
Biomedical Science Tower 3
3501
Dear gromacs users,
I am attempting to simulate a protein with an active site containing to
metals (Ni and Fe). I am trying to mantain the active site structure
constraining bonds, angles and dihedrals.
When I simulate the active site alone in water, it remains stable. When I
insert the active
Hello Justin,
I am running 2,000,000 time steps for the actual MD run (4,000 ps).
Depending on how many solvent molecules I start with, I get slightly
different results. Do you think its ok to run several different tests
and take the average? Or perhaps take the end results of a shorter MD
run
Dear gmx-users,
I have two questions regarding data.xvg file that is used as an input for
g_kinetics. According to manual, this file contains data that can be
interpreted as an indicator for folding. My questions are:
- Does it contain columns of data for different temperatures that are
indicated
Is there any similar script to change it for this reason?
On Fri, Jan 27, 2012 at 11:26 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Dariush Mohammadyani wrote:
Hi all,
I have two files (Topology and Parameter files) in NAMD format (*.inp). I
am going to use them in GROMACS.
Can you
Hi
I've been attempting to use the GPU enabled version of gromacs to run
implicit solvent simulations, but I've run into an odd problem. I have
downloaded and can run the benchmark simulations from the gromacs website,
and reproduce the speeds reported there. However, when I edit the MDP
files to
Sorry to hear that, as I have had the same problem for over four
months (OpenMM 3+, Gromacs 4.5.4+, Cuda 4, etc.). No one ever got
back to me, and I just abandoned Gromacs for Amber (who's GPU
accelerated code base compiles and works).
I would be interested to hear if the intervening time, if a
Hi,
I am working with DOPC lipid molecules, I was searching the literature for the
value of the diffusion coeffecient for DOPC. I could not find one. can some one
tell me what the value is is it close to (8.6 ± 0.2) × 10−12 m2/s?
Ramya Parthasarathi
ramya.sar...@aol.com
--
gmx-users
Fabian Casteblanco wrote:
Hello Justin,
I am running 2,000,000 time steps for the actual MD run (4,000 ps).
Depending on how many solvent molecules I start with, I get slightly
different results. Do you think its ok to run several different tests
and take the average? Or perhaps take the
Dariush Mohammadyani wrote:
Is there any similar script to change it for this reason?
If there is one that exists, it may have been posted to the User Contributions
page of the Gromacs website. If not, maybe someone will post one for you.
I've seen this question asked before with no
Matthew Lardy wrote:
Sorry to hear that, as I have had the same problem for over four
months (OpenMM 3+, Gromacs 4.5.4+, Cuda 4, etc.). No one ever got
back to me, and I just abandoned Gromacs for Amber (who's GPU
accelerated code base compiles and works).
I would be interested to hear if
Hi all,
I was trying to extend my simulation but I used the wrong .tpr file when I
called mdrun_mpi. I didn't catch it in time and my checkpoint files were
overwritten. Now I've used GROMPP to extend the simulation (as directed in
On Thu, Jan 26, 2012 at 7:20 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 27/01/2012 12:35 PM, Naomi Fox wrote:
I would like to print out a list of non-bonded interactions and their
associated LJ-potentials and coulombic potentials.
I tried g_energy, but couldn't figure out the
Naomi Fox wrote:
On Thu, Jan 26, 2012 at 7:20 PM, Mark Abraham mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au wrote:
On 27/01/2012 12:35 PM, Naomi Fox wrote:
I would like to print out a list of non-bonded interactions and
their associated LJ-potentials and
On Fri, Jan 27, 2012 at 12:22 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Naomi Fox wrote:
On Thu, Jan 26, 2012 at 7:20 PM, Mark Abraham
mark.abra...@anu.edu.aumailto:
mark.abra...@anu.edu.**au mark.abra...@anu.edu.au wrote:
On 27/01/2012 12:35 PM, Naomi Fox wrote:
I would
Naomi Fox wrote:
On Fri, Jan 27, 2012 at 12:22 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Naomi Fox wrote:
On Thu, Jan 26, 2012 at 7:20 PM, Mark Abraham
mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au
Thanks Justin!
There is one script in User Contributions page, but it does not work.
I totally changed my way, I will use NAMD in this case...
On Fri, Jan 27, 2012 at 2:11 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Dariush Mohammadyani wrote:
Is there any similar script to change it for
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