I've gone to conclusion that simulation with 1 or 2 GPU simultaneously gave
me the same performance
mdrun -ntmpi 2 -ntomp 6 -gpu_id 01 -v -deffnm md_CaM_test,
mdrun -ntmpi 2 -ntomp 6 -gpu_id 0 -v -deffnm md_CaM_test,
Doest it be due to the small CPU cores or addition RAM ( this system has 32
with gcc to optimize for the CPU
your are building on or e.g. -march=corei7-avx-i for Intel Ivy Bridge
CPUs.
--
Szilárd Páll
On Mon, Nov 4, 2013 at 12:37 PM, James Starlight jmsstarli...@gmail.com
wrote:
Szilárd, thanks for suggestion!
What kind of CPU optimisation should I take into account
in the same regime as in the 2) so its also gave me 22ns/day for
the same system.
How the efficacy of using of dual-GPUs could be increased?
James
2013/11/5 Richard Broadbent richard.broadben...@imperial.ac.uk
Dear James,
On 05/11/13 11:16, James Starlight wrote:
My suggestions:
1
to use the -march (or equivalent)
compiler flag for CPU optimization.
Cheers,
--
Szilárd Páll
On Sun, Nov 3, 2013 at 10:01 AM, James Starlight jmsstarli...@gmail.com
wrote:
Dear Gromacs Users!
I'd like to compile lattest 4.6 Gromacs with native GPU supporting on my
i7
cpu with dual
Dear Gromacs Users!
I'd like to compile lattest 4.6 Gromacs with native GPU supporting on my i7
cpu with dual GeForces Titans gpu mounted. With this config I'd like to
perform simulations using cpu as well as both gpus simultaneously.
What flags besides
cmake .. -DGMX_GPU=ON
?
James
2013/5/29 James Starlight jmsstarli...@gmail.com
Dear Dr. Pall!
Thank you for your suggestions!
Asumming that I have budget of 5000 $ and I want to build gpu-based
desktop on this money.
Previously I've used single 4 core i5 with GTX 670 and obtain average 10
ns\day performance
and temperature (using SD as the thermostat and 2ps coupling). Is there
any other Gromacs build-in tools on what I should paid more attention
during investigation stability of the system with VS ?
James
2013/6/2 Mark Abraham mark.j.abra...@gmail.com
On Sun, Jun 2, 2013 at 4:56 PM, James
of superiority are in model systems that are not particularly chaotic.
As the system gets more chaotic, it matters less.
I would go with md, nose-hoover (w/o chains), and Parrinello-Rahman
with semiisotropic scaling.
On Sat, Jun 1, 2013 at 1:07 AM, James Starlight jmsstarli...@gmail.com
wrote
Mark,
could you also provide me with some examples when usage of VS could give
artifacts in simulations ?
In particular I'm interesting in usage of VS on hydrogens with membrane
proteins.
James
2013/6/1 James Starlight jmsstarli...@gmail.com
Thanks for so detailed explanation!
I've also
31, 2013 at 5:19 PM, James Starlight jmsstarli...@gmail.com
wrote:
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
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
times )
James
2013/5/30 James Starlight jmsstarli...@gmail.com
Also some questions about corrections in the mdp besides the time-step
file which should be included with the VS.
1) What constrains algorithm should I use ?
typically I use
; Bond parameters
constraint_algorithm = lincs
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
should use only weaker coupling during productions runs (I cant use
Parinello;s barostat with such options too)
Thanks for help
James
2013/5/31 James Starlight jmsstarli...@gmail.com
Dear Gromacs users!
I'd like to perform simulation of the membrane protein in lipid-water
system using Nose
negative side-effects
of the inclusion of VSITES might occur in simulation ?
James
2013/5/30 Mark Abraham mark.j.abra...@gmail.com
Manual 6.7?
On Thu, May 30, 2013 at 7:05 AM, James Starlight jmsstarli...@gmail.com
wrote:
Dear Gromacs users!
In some discussions I've noticed that people told
heavy atom-H bonds)
constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
2) Should I vary tau_t constant assuming that I use SD integrator as the
thermostat ( I'm using 2 ps ) ?
2013/5/30 James Starlight jmsstarli...@gmail.com
Dear Gromacs users!
In some discussions I've noticed that people told about usage of virtual
sites which allow to increase time step of the simulation of such systems.
From manual and tutorial its not quite understand for me how with inclusion
of such dummy atoms (which can be used to reduce
that the GTX 680
may not be the best option.
Date: Mon, 27 May 2013 14:14:51 +0400
From: James Starlight jmsstarli...@gmail.commailto:
jmsstarli...@gmail.com
Subject: Re: Re: Re: [gmx-users] GPU-based workstation
To: Discussion list for GROMACS users gmx-users@gromacs.orgmailto:
gmx
, but tried simple large 800 amino, 25,000
solvent
eq (NVT or NPT) runs and they clock at around 1 hour real for say 50 ps
eq's
Stephan
Gesendet: Samstag, 25. Mai 2013 um 07:54 Uhr
Von: James Starlight jmsstarli...@gmail.com
An: Discussion list for GROMACS users gmx-users
point
not worth the money yet, but if you have the money? as I've been browsing.
Also, the sim I did on the cluster was 180-190,000 atoms so the exact same
performance the other person had.
Stephan
*Gesendet:* Samstag, 25. Mai 2013 um 15:19 Uhr
*Von:* James Starlight jmsstarli...@gmail.com
the same, but
still need the board, ram etc...
Mostly just to dream about, they say you can order them with radiation
shielding as well...so...
Stephan Watkins
*Gesendet:* Freitag, 24. Mai 2013 um 13:17 Uhr
*Von:* James Starlight jmsstarli...@gmail.com
*An:* Discussion list for GROMACS
, using just the CPU I get it to run 5-10
minutes real for 1 ns sim, but tried simple large 800 amino, 25,000
solvent eq (NVT or NPT) runs and they clock at around 1 hour real for say
50 ps eq's
Stephan
Gesendet: Samstag, 25. Mai 2013 um 07:54 Uhr
Von: James Starlight jmsstarli
Dear Gromacs Users!
I'd like to build new workstation for performing simulation on GPU with
Gromacs 4.6 native cuda support.
Recently I've used such setup with Core i5 cpu and nvidia 670 GTX video
and obtain good performance ( ~ 20 ns\day for typical 60.000 atom system
with SD integrator)
Now
tests of new Gromacs 4.6
with different hardware setups ?
Thanks for help
James
2013/5/24 James Starlight jmsstarli...@gmail.com
Dear Gromacs Users!
I'd like to build new workstation for performing simulation on GPU with
Gromacs 4.6 native cuda support.
Recently I've used such setup
Dear Gromacs users!
I want to find possible way for the conversion of the set of the Gromacs's
xtc trajectories to the DCD format.
The only possible way that I know for such conversion is the VMD. But it's
very routine for the big set of the XTC's inputs.
Thanks for help,
James
--
gmx-users
Dear Gromacs users!
I have performed long md run. From the production trajectory by means of
trjconv -f md_.trr -s cam.tpr -dt 10 -e 300 -sep -o ./pdbs/.pdb # extract
conformers from first 300 ps each 10ps steps
I've extracted 10 conformers in the desired time step
Than when I perform MD on
this warning the correct way.
Mark
On Fri, May 3, 2013 at 8:18 AM, James Starlight jmsstarli...@gmail.com
wrote:
Dear Gromacs users!
I have performed long md run. From the production trajectory by means of
trjconv -f md_.trr -s cam.tpr -dt 10 -e 300 -sep -o ./pdbs/.pdb #
extract
for each conformers). Should I re-assign
velocities for each conformer (addition nvt run) to fix it ?
James
2013/5/3 Mark Abraham mark.j.abra...@gmail.com
On Fri, May 3, 2013 at 11:15 AM, James Starlight jmsstarli...@gmail.com
wrote:
Mark,
thanks for suggestions
as I've told previously
mark.j.abra...@gmail.com
EM has no velocities, by definition. Does the EM mdrun write a .gro file
with velocities? If so, that's a bug.
On Fri, May 3, 2013 at 2:51 PM, James Starlight jmsstarli...@gmail.com
wrote:
I've noticed that the minimized conformers no longer has the velocities
)
for the umbrella's NPT+MD. What the input data in the mdp files must be in
that case using CV?
James
2013/4/30 Justin Lemkul jalem...@vt.edu
On 4/30/13 1:38 PM, James Starlight wrote:
Justin,
could you also tell me
1) what difference should be expected from the umbrella sampling run with
(as I
The problem was solved by adding -pbc mol -ur compact flags to the trjconv.
So the problems were indeed in pbc conditions
James
2013/5/3 Mark Abraham mark.j.abra...@gmail.com
On Fri, May 3, 2013 at 3:17 PM, James Starlight jmsstarli...@gmail.com
wrote:
Mark,
but if I run npt
Dear Gromacs users!
I have a question about umbrella sampling simulation based on the Justin's
tutorial.
According to the tutorial after definition of the set of conformers
extracted from the pulled trajectory I should run N equilibrating
simulations and N productions runs. In the tutorial I've
functional
transitions?
Thanks for help,
James
2013/4/30 Justin Lemkul jalem...@vt.edu
On 4/30/13 10:58 AM, James Starlight wrote:
Dear Gromacs users!
I have a question about umbrella sampling simulation based on the Justin's
tutorial.
According to the tutorial after definition of the set
?
James
2013/4/23 Justin Lemkul jalem...@vt.edu
On 4/23/13 10:18 AM, James Starlight wrote:
Justin,
as the example I have 2 systems consisted of receptor completed with 2
different ligands.
After 100ns of production run I've realized that both of that ligands has
the same degree
Justin Lemkul jalem...@vt.edu
On 2/7/13 5:15 AM, James Starlight wrote:
Justin,
Thanks again for suggestion. I've found that g_mindist is exactly what
I need. I'm not quite sure how I could use that tools to find all
possible interactions between my ligand and several polar residues
Dear Gromacs users!
I wounder to know if it possible to simple estimate drug affinity by mean
of MD simulation? As I know the drug's property is based on the free energy
change of bound-unbound ligand. So It seems that Justin's tutorial (free
energy calculations) might be usefull if it would not
Justin,
and what exactly method from that list could be most easily performed in
gromacs for the estimation of the affinity of small mollecules to the
membrane receptors?
2013/4/14 Justin Lemkul jalem...@vt.edu
On 4/14/13 2:13 AM, James Starlight wrote:
Dear Gromacs users!
I wounder
, 2013 at 2:12 PM, James Starlight jmsstarli...@gmail.com
wrote:
During the past few days I've tried to make parametrization of any
heme-containing cythochromes and always failed with the huge errors about
missing parameters. Could someone provide me with such params (i suppose
it
should
for such parameters suitable for charm but
didnt find anything.
Does anybody here tried to simulate cytochrome ?
James
2013/4/12 James Starlight jmsstarli...@gmail.com
by the way also I've tried to make model of cytochrome p450 in charmm. In
that case heme have only one coordinate bond with the side chain
also I found such parameters in the native charm format (.prm)
could you provide me with some script for conversion of tpr to itp? I could
do such topology for cytochrome and add it to the contribution :)
James
2013/4/12 James Starlight jmsstarli...@gmail.com
I forgot to point out that when I
) for any ful-atomic force field? Finally I've not found in mailing
list any possible sollution of the same problems.
James
2013/4/4 James Starlight jmsstarli...@gmail.com
It was strange for me the big number of such errors :)
May the construction of new scheme for the hydrogens in the .hdb
or charm). Might it be relevant ? Should I switch to
the spc water with the amber ?
James
2013/4/8 Justin Lemkul jalem...@vt.edu
On Mon, Apr 8, 2013 at 7:50 AM, James Starlight jmsstarli...@gmail.com
wrote:
In literature I found that the ussage of 1.0 cutoffs should give good
results
behaviour of
the system is very 'straitjacketed' - its likely my protein placed in the
compact crystal environment preventing its dynamics.
James
2013/4/9 Mark Abraham mark.j.abra...@gmail.com
On Tue, Apr 9, 2013 at 9:59 AM, James Starlight jmsstarli...@gmail.com
wrote:
By the way during simulation
In literature I found that the ussage of 1.0 cutoffs should give good
results but in the antechamber manual I've seen that usages of 1.2 cutoofs
( with GAFF) should be used. So what cut-offs should I use for
protein-ligand complexes done in amber ? (assuming that I simulate my
system in the berger
Dear Gromacs Users!
I'm looking for cut-offs parameters which would be suitable for the
simulation of the membrane proteins (bergers united-atom lipids) with the
amber-99 force fields (full-atomic protein representation). I'd be thankful
to anyone who can provide me with such cut-offs for vdw as
? :-)
Mark
On Sat, Apr 6, 2013 at 8:24 AM, James Starlight jmsstarli...@gmail.com
wrote:
Dear Gromacs Users!
I'm looking for cut-offs parameters which would be suitable for the
simulation of the membrane proteins (bergers united-atom lipids) with the
amber-99 force fields (full-atomic
Dear Gromacs users!
I want to simulate Cytochrome C in complex with HEM using NMR full-atom
structure of that protein as the starting conformation and charm36 force
field's parameters.
in the charm36 ff I've found parameters for HEM but I have not found params
for the hydrogens (in the
to the
rest of the protein ( as in the case of GFP or rhodopsin). So the
parameters for the hem should be included as the any other diffusiable
ligand (as the separate itp file) in topology, should'n it?
James
2013/4/3 Justin Lemkul jalem...@vt.edu
On Wed, Apr 3, 2013 at 8:24 AM, James Starlight
HEME included in the rtps)
I still need a example of properly parametrized hem complexed with any
cytochrome :)
James
2013/4/3 James Starlight jmsstarli...@gmail.com
hmm
I've done parametrization of the hem using standart charmm36 parameters
but indeed there is some confusing
-cytochrome complex (it looks like NMR
structure) but why that errors occured ?
James
2013/4/3 James Starlight jmsstarli...@gmail.com
sorry it was mistake :)
assuming that heme is covalently bonded to the cytochrome by means of 2
cysteines how should I define such bindings (assuming
in the residuetype.dat as the part of the protein?
Finally I'll be thankful to everyone who could provide me with the any
cytochrome properly parametrized in charmm :)
James
2013/4/3 Justin Lemkul jalem...@vt.edu
On Wed, Apr 3, 2013 at 10:27 AM, James Starlight jmsstarli...@gmail.com
wrote:
I've
Dear Gromacs Users!
Could someone provide me with the tutorial example with the algoritm
of ussing Nose-Hover chains thermostat. In particular It's not quite
understood for me how I should define number of chains in the mdp file
and how that number would affect on simulation performance (E.g In
Dear Gromacs users!
I'd like to perform MD simulation of the membrane protein parametrized
in Amber99sb force field. Could you tell me what cut-off patterns
should I use for such simulation ?
James
--
gmx-users mailing listgmx-users@gromacs.org
searches by your own and read
_carefully_ the documentation:
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations?highlight=extend
On 02/14/2013 08:13 AM, James Starlight wrote:
Dear Gromacs Users!
I have completed 100ns md trajectory.
I 'd like to go on that simulation
previous.cpt
What it's the right thing to do.
On 02/14/2013 10:11 AM, James Starlight wrote:
I've already tried to do it in accordance to that instructions!
firstly I've created new tpr file where I changed only duration of my
simulation
grompp -f ./mdps/md_sd.mdp -n index -c old.tpr -o
Dear Gromacs Users!
I have completed 100ns md trajectory.
I 'd like to go on that simulation adding extra 100 ns to the existing
trajectory (with appending of both trajectories in single file during
that simulation)
If I do it just via
mdrun -v -cpi md -deffnm md
the simulation have not gone
Dear all!
1) I'd like also to know more about algorithm of the reference
structure choosing.
Commonly I'm using
g_covar -f md.trr -s md.tpr
fur PCA of the md trajectory ( here md.tpr is the protein topology and
md.trr is the protein only trajectory)
and
g_covar -f ensemble.pdb -s ref.pdb
Hi Albert!
As I understood your correctly you have run simulations with your 2
GPU cards on Gromacs-beta but could not do it with final version
havent it?
Could you tell me how you installed both GPU in your work-station?
Have you used SLI ? ( I've heard that gromacs is not suported the
Justin Lemkul jalem...@vt.edu:
On 2/6/13 2:54 PM, James Starlight wrote:
by the way could someone provide me with some simple tutorial of the
usage of the CGenFF for construction ITP topology for charmm f.f ?
Also I still could not found any simple way to monitor dynamics of the
non
of explicit membrane etc)?
Thank you for help again,
James
2013/2/7 Albert mailmd2...@gmail.com:
On 02/07/2013 11:03 AM, James Starlight wrote:
Hi Albert!
As I understood your correctly you have run simulations with your 2
GPU cards on Gromacs-beta but could not do it with final version
stacking interactions
could be monitored?
James
2013/2/5, James Starlight jmsstarli...@gmail.com:
Dear Gromacs users!
At present time I'm simulating protein-ligand complexes parametrized
in Charmm force field. In particular I'm not quite sure aboout
correctness of params made for my ligands
other than g_saltbr gromacs tools be used for that
(E,g g_dist ) ?
James
2013/2/3 Justin Lemkul jalem...@vt.edu:
On 2/3/13 1:01 AM, James Starlight wrote:
Justin,
thanks again for suggestions.
I'm not quite sure how I can use tpbconv -zeroq. For example I want to
reduce charges of all
:
On 2/2/13 12:18 AM, James Starlight wrote:
Justin,
I suppose that the ussage of the sub-set of trajectories is suitable
when you've already known possible salt-bridge pairs. But that time
I'd like to obtain that information from my trajectory.
E.g I have membrane-embedded protein which
Dear Gromacs users!
I have trajectory from which I want to investigate dynamics of all
possible salt bridges (E.g distance between adjacent + and - charged
residues) of my protein during the simulation
As I understood ussage of g_saltbr -t -sep could be suitable for such
thing but I'm not sure
into account that my protein
is membrane-bound where helixes are situated closely than in
water-soluble proteins) but again that produced many wrong pairs.
James
2013/2/2 Justin Lemkul jalem...@vt.edu:
On 2/1/13 3:22 PM, James Starlight wrote:
Dear Gromacs users!
I have trajectory from
either with gmxcheck or trjconv -dump -1 (this will print out the
time of the last frame).
2- -skip # takes only every #th frame.
Best regards
Sebastian
On 29.01.2013 07:28, James Starlight wrote:
Dear Gromac's users!
I have long trajectory with small intervals between individual
in gromos-54a7 united atom
( the same number of lipids and water) ff with 1.2 cut-offs I didnt
observed any decrease of the cutoffs.
James
2013/1/29 Justin Lemkul jalem...@vt.edu:
On 1/29/13 2:19 AM, James Starlight wrote:
One important point:
in that simulations I've used decreased cut
/b2armembrane.png
James
2013/1/28 Justin Lemkul jalem...@vt.edu:
On 1/28/13 2:45 AM, James Starlight wrote:
Dear Gromacs Users!
I'm simulating membrane receptor embedded in the explicit membrane
using charmm36 ff.
My simulation setup consist of
; Compound#mols
Protein 1
iso
Justin,
yes, 2 A for C atoms.
The dims are 8.68740 8.41864 10.0
James
2013/1/28 Justin Lemkul jalem...@vt.edu:
On 1/28/13 8:30 AM, James Starlight wrote:
Justin,
Below you can see graph representation of my system after energy
minimisation ( that case system was filled up
for such simulation ?
James
2013/1/28 Justin Lemkul jalem...@vt.edu:
On 1/28/13 8:45 AM, James Starlight wrote:
Justin,
yes, 2 A for C atoms.
The dims are 8.68740 8.41864 10.0
Well, with such a dramatic change, it should be fairly easy to simply watch
the trajectory and see
Dear Gromac's users!
I have long trajectory with small intervals between individual
time-steps. Using editconf I'd like:
1- To extract last frame in pdb from my trajectory
(e.g for extraction of the first frame I'm using but its not working
with -dump -1 )
2- To convert my trajectory into xtc
2013/1/29 James Starlight jmsstarli...@gmail.com:
Its intresting that on the same system which was equilibrated longer
the decrease on the Z dim was smaller (from 10 to 9nm). By the way
does it possible to simulate membrane proteins (with explicit
membrane) in the nvt enssemble without explicit
Dear Gromacs Users!
I'm simulating membrane receptor embedded in the explicit membrane
using charmm36 ff.
My simulation setup consist of
; Compound#mols
Protein 1
iso 1
POPC 228
SOL 11713
NA 66
CL 70
I've done
trajectories should look the
same. If they don't, then your two ensembles differ.
Mark
James
2013/1/25 Mark Abraham mark.j.abra...@gmail.com:
On Tue, Jan 22, 2013 at 8:22 PM, James Starlight jmsstarli...@gmail.com
wrote:
Dear Gromacs users!
There is some bug with g_anaeig
Dear Gromacs Users!
In the gromacs-4.6 version I have some problems with the trp files
obtained after reduction of atom subset via
tpbconv -f initial.tpr -n index -o reduced.tpr
where in index file reduced atom sub set was defined ( e.g c-alpha
atoms from the protein only )
then I'm using
After switching to gcc-4.6 I've obtained that error on the first step
of gromacs compilation
[ 0%] Building NVCC (Device) object
src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o
gcc: error trying to exec 'cc1plus': execvp: No such file or directory
CMake Error
thread
Using 2 OpenMP threads
No GPUs detected
I've installed cuda-5.0 with driver
NVRM version: NVIDIA UNIX x86_64 Kernel Module 304.54 Sat Sep 29
00:05:49 PDT 2012
that system works fine with the recent nvidia GPU's but has no support
for GeForce 9500.
James
2013/1/24, James Starlight
structures)
How it could be fixed ?
2013/1/24 Justin Lemkul jalem...@vt.edu:
On 1/24/13 7:21 AM, James Starlight wrote:
Dear Gromacs Users!
In the gromacs-4.6 version I have some problems with the trp files
obtained after reduction of atom subset via
tpbconv -f initial.tpr -n index -o
...@cbr.su.sewrote:
On Thu, Jan 24, 2013 at 3:28 PM, Justin Lemkul jalem...@vt.edu wrote:
On 1/24/13 9:23 AM, James Starlight wrote:
oh that was simply solved by upgrading of G++ :)
the only problem which remains is the missing of support of mu GPU :(
That time I've tried to start simulation on simply
...@vt.edu:
On 1/24/13 9:44 AM, James Starlight wrote:
Justin,
thanks. I've not known that posres were defined in the tpr file as well.
Sure, how else would mdrun know what to do? :)
By the way could you make your suggestion in my another topic which
I've posted some days ago about
have
performance similar to your at the GTX 680. I't intresting to me is
there any reason to buy modern tesla card ( which prise is 2000$ )
James
2013/1/25 Szilárd Páll szilard.p...@cbr.su.se:
On Mon, Jan 14, 2013 at 7:20 PM, James Starlight
jmsstarli...@gmail.comwrote:
1)As I understood
g_covar in both cases
produce apropriate cov.matrix and the problem only in g_anaeig .
James
2013/1/25 Mark Abraham mark.j.abra...@gmail.com:
On Tue, Jan 22, 2013 at 8:22 PM, James Starlight
jmsstarli...@gmail.comwrote:
Dear Gromacs users!
There is some bug with g_anaeig the souce of which
Szilárd,
Today I've tried to re-install cuda+gromacs and do apt-get
distr-upgrade but the same error was obtained during gromacs
compilation. By the way where I could provide --add-needed option ?
James
2013/1/21 Szilárd Páll szilard.p...@cbr.su.se:
Szilárd
--
gmx-users mailing list
Szilárd Páll szilard.p...@cbr.su.se:
On Tue, Jan 22, 2013 at 12:45 PM, James Starlight
jmsstarli...@gmail.comwrote:
Szilárd,
Today I've tried to re-install cuda+gromacs and do apt-get
distr-upgrade but the same error was obtained during gromacs
I'm don't see how does the distribution upgrade
Dear Gromacs users!
There is some bug with g_anaeig the souce of which I could not fully
understand. I have problems when I perform PCA of X-ray data set.
Below you can my workflow.
g_covar -f b2ar_xray_coors.pdb -s ref.pdb -o PCA_eigenval.xvg -v
PCA_eigenvec.trr -av PCA_average.pdb -last
Dear Gromacs Users!
I want to simulate sensory rhodopsin which in the ground-state
contains cys-retinal covalently bonded to the polypeptide mainchain of
photoreceptor via Shiff base. Now I'm looking for reasonable
parameters of that retinal cofactor group for charmm ( 27 or 36 force
field) I'll
Dear Developers!
Today in the download section on gromacs web I've found 2 new verions
of gromacs ( 4.6 and 4.5.6) aviable for downloading. Does it final
releases and in what they differs?Have both of them native GPU
support ?
James
2013/1/17 James Starlight jmsstarli...@gmail.com:
Thank you
2013/1/6 Bogdan Costescu bcoste...@gmail.com:
On Sun, Jan 6, 2013 at 1:44 PM, James Starlight jmsstarli...@gmail.com
wrote:
I mean absence of exponential factor in the C6 term :)
So to change the vdw radius of the specified atom I should to varry
both c6 and c12 shouldn't it ?
Hmm, to me
must to
increase c12 or decreace C6 terms. Does it correct in general ?
2013/1/17 Bogdan Costescu bcoste...@gmail.com:
On Thu, Jan 17, 2013 at 10:59 AM, James Starlight
jmsstarli...@gmail.com wrote:
thank you for so detailed explanation.
You're welcome. Now it's up to you to use it :)
Now
Dear Gromacs Developers!
Using sd1 integrator I've obtain good performance with the core-5 +
GTX 670 ( 13ns\per day) for the system of 60k atoms. That results on
30% better than with the sd integrator.
Buit on my another work-station which differs only by slower GPU ( GT
640). I've obtained
:
On Thu, Jan 17, 2013 at 1:51 PM, James Starlight jmsstarli...@gmail.com
wrote:
So if I have force field with the C6/C12 terms (instead of
sigma\epsilon) I need to express sigma (which correspond to the Rmin
in LJ equation) as the (C12/C6)^0.5. Than if I want to increase sigma
( and consequently
avoid it ?
2013/1/17 James Starlight jmsstarli...@gmail.com:
Dear Gromacs Users!
I'm simulatting open to close transition of calmodulin by means of
essential dynamics sampling. When my protein reaches closed state
(this time both ef hands domains aproach each other) I've obtain set
of lincs
Lemkul jalem...@vt.edu:
On 1/17/13 9:51 AM, James Starlight wrote:
Bogdan,
It's not clear for me how I could change sigma with fixed epsilon in
case of using (A/R)^12-(A/R)^6 form of LJ. In that case sigma and
epsion depends both on A and B so changing A or B we will influence
both sigma
Justin,
so its exacly what I mean! I dont find any relationship between LJ
equation in any form and vdw radius of atom. But is it possible to
modify vdw radius exactly ? E.g I have united atom as a node which
vdw must be 1.5 A. I want to decrease it to 1 A. What should I do
for it ?
James
Hi all!
I've also done some calculations with the SD integraator used as the
thermostat ( without t_coupl ) with the system of 65k atoms I obtained
10ns\day performance on gtc 670 and 4th core i5.
I haventrun any simulations with MD integrator yet so It should test it.
James
2013/1/15 Szilárd
people implementing new features may wish to consider
that in their choice to write code :-)
Mark
On Tue, Jan 15, 2013 at 2:26 PM, James Starlight
jmsstarli...@gmail.comwrote:
Dear Gromacs developers!
There is well-known plugin plumed which can be used for implementation
of meta-dynamics
Dear Gromacs Users!
I'd like to know if it's possible to obtain some values from do_dssp
except the graph diagrams of the ss dynamics ? For example I wounder
to know values of how many residues were in helix, sheet or coil
conformation during my simulation ?
By the way during analysis of the
it.
I'm using gromacs-4.6-beta 3 with dssp 2.0.3
James
2013/1/15 Justin Lemkul jalem...@vt.edu:
On 1/15/13 3:19 AM, James Starlight wrote:
Dear Gromacs Users!
I'd like to know if it's possible to obtain some values from do_dssp
except the graph diagrams of the ss dynamics ? For example I
Justin, thanks both options works perfect.
James
2013/1/15 Justin Lemkul jalem...@vt.edu:
On 1/15/13 7:13 AM, James Starlight wrote:
Justin,
I want to obtain timescale on X as well as number of residues on Y
on the xmp graph . By default that graph has not legend so it's hard
method).
James
2013/1/15 James Starlight jmsstarli...@gmail.com:
Dear Gromacs Users!
Recently I've completed Umbrella sampling tutorial presented on the
Justin's web. I'd like to use that teqnique as the engine for
enhansing of conformational sampling of some monomeric proteins
(starting
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