On 2013-06-01 02:24, Marcelo Vanean wrote:
Hello to everyone. In version 4.5.5, calculating the viscosity with the
command g_energy -vis, the generated files (eviscoi.xvg, eviscoi.xvg and
visco.xvg) are inconsistent. The file evisco.xvg, for example, gives a
value of zero for viscosity using the
Performing 5ns simulation after 2 ns equilibration in NPT ensemble (MTTK
barostat 5ps coupling ) I've observed non-physical behaviour of my system
with the constant drift of the protein molecule as the rigid body in the
y-z plane
Energy Average Err.Est. RMSD Tot-Drift
The conversion is in ffnonbonded.itp. However, unless you plan to modify
the forcefield you shouldn't need this.
Richard
On 01/06/2013 00:57, "Hari Pandey" wrote:
>Dear Gromacs users,
>
>I am a new user and I have some questions
> I confused about indexing. in atomtypes.atp clearly we can kn
Hello to everyone. In version 4.5.5, calculating the viscosity with the
command g_energy -vis, the generated files (eviscoi.xvg, eviscoi.xvg and
visco.xvg) are inconsistent. The file evisco.xvg, for example, gives a
value of zero for viscosity using the Einstein relation. Another question
in 4.0.7,
Dear Gromacs users,
I am a new user and I have some questions
I confused about indexing. in atomtypes.atp clearly we can know the index
is for what kind of atom but in ffbondedtype.itp there is different kind of
the indexing so I confused how do i pathch the force field .
Some are obvious
Could be a bug, but unless you can reproduce it with 4.5.7 or 4.6.x then
you won't get much help there :-)
Mark
On Fri, May 31, 2013 at 9:56 PM, Parker de Waal wrote:
> Hi Everyone,
>
> I'm trying to run energy minimization on my system and I am encountering
> the following error:
>
> Getting L
On Fri, May 31, 2013 at 11:30 AM, Sainitin Donakonda wrote:
> Hi Mark,
>
> I forgot to mention about simulation it is protein ligand simulation which
> contains one protein and ligand with 2 solute molecules..
So assuming you mean "solvent", about 60K atoms.
> and regarding
> hardware of c
Hi Everyone,
I'm trying to run energy minimization on my system and I am encountering
the following error:
Getting Loaded...
Reading file em.tpr, VERSION 4.5.5 (single precision)
Starting 16 threads
Loaded with Money
Will use 10 particle-particle and 6 PME only nodes
This is a guess, check the
Dear Thomas,
Thanks a lot again for great reply. Please clarify this also,
>> If one uses only 'Y N N' B would only move along the x-axis due to the
pull, but could move freely in the yz-plane
>>You never want to use the pull-code and 'pull_dim = N N N'
>>This would mean that there is no force ac
Dear Gromacs users!
I'd like to perform simulation of the membrane protein in lipid-water
system using Nose-Hover with chains.
>From manual I've found that with such thermostat I should use (1) md-vv
integrator (2) MTTK instead of Parinello's batostat and (3) shake instead
of LINCS.
How doest
For comments to your questions see below.
More general: (somewhat longer than i wanted. Hope you find some answers
here)
Imagine two interacting particles A and B which are alinged to the
x-axis. We take A as the reference group, B as pulled group and put the
origin of the umbrella potential
All these parameters are for Mg2+, forgot to mention.
On Fri, May 31, 2013 at 10:48 PM, tarak karmakar wrote:
> Dear All,
>
> I have a little confusion with the non-bonding parameters conversion from
> OPLS-AA to CHARMM in gromacs.
> If I see the ffnonbonded.itp in both the cases I get the foll
Dear All,
I have a little confusion with the non-bonding parameters conversion from
OPLS-AA to CHARMM in gromacs.
If I see the ffnonbonded.itp in both the cases I get the following numbers
OPLS-GROMACS
Sigma = 0.1644471 nm
Epsilon = (0.875044*4.184) = 3.66118 kJ/mol
On 2013-05-31 15:59, Davide Mercadante wrote:
Dear gmx users,
I am writing to ask why I am getting a dihedral autocorrelation function
(ACF) with negative values. I am trying to calculate the ACF using
g_angle (gromacs 4.5.5) with the following set of flags:
g_angle -f trajectory.xtc -type dihe
3) Also I've already performed small simulation with the time step 5 fs
(defining virtual sites by means of pdb2gmx -vsites and introducing heavy
hydrogens. I've not observed any errors during my simulation. When I've
tried to increase dt up to 7 fs I've obtained warnings according to that I
shoul
Hi All,
Does anybody know which force filed I can use for oxidized lipid or
peroxidated lipid?
You can see the below link to get how fatty acid will change by
peroxidation:
http://en.wikipedia.org/wiki/Lipid_peroxidation
If there is not any, what is the suggestion?
Thanks,
Dariush
--
View th
Dear gmx users,
I am writing to ask why I am getting a dihedral autocorrelation function
(ACF) with negative values. I am trying to calculate the ACF using
g_angle (gromacs 4.5.5) with the following set of flags:
g_angle -f trajectory.xtc -type dihedral -oc acf.xvg -od angdist.xvg -n
angle.ndx
T
Dear Gromacs users!
I have some topologies made for NAMD (param files) which I'd like convert
to the Gromacs itp formats. Could someone provide me with some tools for
such conversion?
Thanks for help,
James
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/lis
Dear Thomas,
Thanks a lot for your time and nice explanation. I was not able to get
specially the pull_start flag but now its quite clear.
I feel sorry, that should be pull_dim = N N N in my case. Also I will be
much thankful if you please can help me to make understand following:
1)
>> If you d
Look also into the manual. But the tutorial is a nice place to start.
For further comments see below:
Dear Lloyd,
I have read that but my system is different
regards,
On Thu, May 30, 2013 at 8:28 PM, lloyd riggs wrote:
>Dear Jiom,
>
>Look at justines tutorial, there's example pull .mdp.
>
Hi Millinda.
I know it is an old post, bt I am not sure if your defaults are correct.
This question is only because I am struggling to make CLAYff work and hence
looking around. So mb you know something I don't.
> [ defaults ]
> ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ
>
Hi Mark,
I forgot to mention about simulation it is protein ligand simulation which
contains one protein and ligand with 2 solute molecules..and regarding
hardware of cluster which is in my university as follows
CPUs AMD Opteron 6274 number of cores 5888 th. peak performance 51.8
TFlop
There are lots of things you might do, but when we don't know what's in the
simulation or anything about the hardware, nobody can tell.
Mark
On Thu, May 30, 2013 at 2:16 PM, Sainitin Donakonda wrote:
> Hi all,
>
> I recently ran 20ns simulation in linux cluster.
>
> Used following script for MD
Hi all,
I recently ran 20ns simulation in linux cluster.
Used following script for MD simulation
#This is the first simulation MD.mdp file contains 20 ns setup
grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
MD_first10.tpr
mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_firs
Hi,
You can only have as many replicas as you have MPI processes available, but
you can find out how to configure your MPI to allow such over-subscription
of your hardware.
Mark
On May 31, 2013 6:28 AM, "Sanku M" wrote:
> Hi,
> I am wondering if there is a way I can use twice more number of r
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