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
gb
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
> Dear James,
>
>
> On 05/11/13 11:16, James Starlight wrote:
>
>> My suggestions:
>>
>
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
> wrote:
> > Szilárd, thanks for suggestion!
> >
> > What kind of CPU opti
arch (or equivalent)
> compiler flag for CPU optimization.
>
> Cheers,
> --
> Szilárd Páll
>
>
> On Sun, Nov 3, 2013 at 10:01 AM, James Starlight
> wrote:
> > Dear Gromacs Users!
> >
> > I'd like to compile lattest 4.6 Gromacs with native GPU supportin
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 -DCUDA_TOOLKIT_ROOT_
?
James
2013/5/29 James Starlight
> 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
>
in energy
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
> On Sun, Jun 2, 2013 at 4:56 PM, James Starlight >w
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
> Thanks for so detailed explanation!
>
> I've a
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
&
13 at 5:19 PM, James Starlight >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.
s and md-vv I
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
> Dear Gromacs users!
>
> I'd like to perform simulation of the membrane protein in lipid-water
> syste
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
t- higher
relaxation times )
James
2013/5/30 James Starlight
> 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
> co
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
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
> Mark,
&g
t possible negative side-effects
of the inclusion of VSITES might occur in simulation ?
James
2013/5/30 Mark Abraham
> Manual 6.7?
>
>
> On Thu, May 30, 2013 at 7:05 AM, James Starlight >wrote:
>
> > Dear Gromacs users!
> >
> > In some discussions I've notice
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 numb
p (3-4000 US$ for an 8-10 gpu board). RAM ordered abroad
> is
> > also cheep, 8 or 16 MB Vs. Shop...I have used 4 GPU's but only on tests
> > software, not Gromacs, so would be nice to see performance...for a small
> 100
> > atom molecule and 500 solvent, using just the
sible price issues, it seems that the GTX 680
> may not be the best option.
>
>
>
> >Date: Mon, 27 May 2013 14:14:51 +0400
>
> >From: James Starlight jmsstarli...@gmail.com>>
>
> >Subject: Re: Re: Re: [gmx-users] GPU-based workstation
>
om an individual 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 Uh
t; software, not Gromacs, so would be nice to see performance...for a small
> 100 atom molecule and 500 solvent, 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 re
n design them though to fit a PCIe slot and run about 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 U
with some bechmark tests of new Gromacs 4.6
with different hardware setups ?
Thanks for help
James
2013/5/24 James Starlight
> Dear Gromacs Users!
>
>
> I'd like to build new workstation for performing simulation on GPU with
> Gromacs 4.6 native cuda support.
> Recently I
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
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
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
> On Fri, May 3, 2013 at 3:17 PM, James Starlight >wrote:
>
> > Mark,
> >
> >
> > but if I run npt equil
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
>
>
> On 4/30/13 1:38 PM, James Starlight wrote:
>
>> Justin,
>>
>>
>> could you also tell me
>> 1) what difference should be expect
> 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 >wrote:
>
> > I've noticed that the minimized conformers no longer has the velocities
&
e for each conformers). Should I re-assign
velocities for each conformer (addition nvt run) to fix it ?
James
2013/5/3 Mark Abraham
> On Fri, May 3, 2013 at 11:15 AM, James Starlight >wrote:
>
> > Mark,
> >
> > thanks for suggestions
> >
> > as I've to
our trjconv frames so that the molecules are whole, you
> will suppress this warning the "correct" way.
>
> Mark
>
> On Fri, May 3, 2013 at 8:18 AM, James Starlight >wrote:
>
> > Dear Gromacs users!
> >
> > I have performed long md run. From the produc
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
functional
transitions?
Thanks for help,
James
2013/4/30 Justin Lemkul
>
>
> 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.
>>
>>
>&g
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
ctory ?
James
2013/4/23 Justin Lemkul
>
>
> 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'
ames
2013/2/7 Justin Lemkul
>
>
> 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
>>
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
>
>
> On 4/14/13 2:13 AM, James Starlight wrote:
>
>> Dear Gromacs users!
>&
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 b
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
> I forgot to point out that when I made topology
rature for such parameters suitable for charm but
didnt find anything.
Does anybody here tried to simulate cytochrome ?
James
2013/4/12 James Starlight
> 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
hu, Apr 11, 2013 at 2:12 PM, James Starlight >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 par
rtps) 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
> It was strange for me the big number of such errors :)
> May the construction of new scheme for the hydrogens in the .hdb file
&
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
> On Tue, Apr 9, 2013 at 9:59 AM, James Starlight
> wrote:
> > By the way during simulation of the membrane-
3p in the amber or charm). Might it be relevant ? Should I switch to
the spc water with the amber ?
James
2013/4/8 Justin Lemkul
> On Mon, Apr 8, 2013 at 7:50 AM, James Starlight >wrote:
>
> > In literature I found that the ussage of 1.0 cutoffs should give good
> > result
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
ark
>
> On Sat, Apr 6, 2013 at 8:24 AM, James Starlight >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
> &
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
n 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
> On Wed, Apr 3, 2013 at 10:27 AM, James Starlight >wrote:
>
> > I've successful
rtions in the geometry of heme-cytochrome complex (it looks like NMR
structure) but why that errors occured ?
James
2013/4/3 James Starlight
> sorry it was mistake :)
>
> assuming that heme is covalently bonded to the cytochrome by means of 2
> cysteines how should I define such bi
HEME included in the rtps)
I still need a example of properly parametrized hem complexed with any
cytochrome :)
James
2013/4/3 James Starlight
> hmm
>
> I've done parametrization of the hem using standart charmm36 parameters
> but indeed there is some confusing with the hydrogen
ed 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
> On Wed, Apr 3, 2013 at 8:24 AM, James Star
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 aminoacid
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
http://lists.gromacs.org/mailman/listinfo/gmx-
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
l
Dear Gromacs Users!
During preparation of the protein-ligand complex (manual placement of
the ligand into the ligand-binding pocket (based onto known x-ray
data) I've forced with the overlap of some polar sidechains of the
ligand interiour with big aromatic group of the ligand itself. I've
tried
Dear Gromacs users!
Commonly I analyze my MD trajectories by means of covariance analysis
(projections onto some PC made by g_anaiegn).
>From that projections I've often observe several highly populated
basins corresponded to the most populated regions of the collective
space where the system spe
revious.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 d
es 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 traje
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 o
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
for
,
presence of explicit membrane etc)?
Thank you for help again,
James
2013/2/7 Albert :
> 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 Gr
for help
James
2013/2/7 Justin Lemkul :
>
>
> 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
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
simulati
stacking interactions
could be monitored?
James
2013/2/5, James Starlight :
> 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 lig
Could other than g_saltbr gromacs tools be used for that
(E,g g_dist ) ?
James
2013/2/3 Justin Lemkul :
>
>
> 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
t;
> 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
well as taking 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 :
>
>
> On 2/1/13 3:22 PM, James Starlight wrote:
>>
>> Dear Gromacs us
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 i
uch system 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 :
>
>
> On 1/29/13 2:19 AM, James Starlight wrote:
>>
>> One important point:
>>
>> in th
rajectory 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
James
2013/1/29 James Starlight :
> 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 explici
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 w
for such simulation ?
James
2013/1/28 Justin Lemkul :
>
>
> 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 s
Justin,
yes, 2 A for C atoms.
The dims are 8.68740 8.41864 10.0
James
2013/1/28 Justin Lemkul :
>
>
> On 1/28/13 8:30 AM, James Starlight wrote:
>>
>> Justin,
>>
>> Below you can see graph representation of my system after energy
>> minimisatio
/b2armembrane.png
James
2013/1/28 Justin Lemkul :
>
>
> 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
>
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
d on the other's eigensystem. If the
> eigensystems are equivalent, then the filtered trajectories should look the
> same. If they don't, then your two ensembles differ.
>
> Mark
>
> James
>>
>> 2013/1/25 Mark Abraham :
>> > On Tue, Jan 22, 2013 at 8:22
g_covar in both cases
produce apropriate cov.matrix and the problem only in g_anaeig .
James
2013/1/25 Mark Abraham :
> On Tue, Jan 22, 2013 at 8:22 PM, James Starlight
> wrote:
>
>> Dear Gromacs users!
>>
>>
>> There is some bug with g_anaeig the souce of whic
400$ gtx 670 I 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 :
> On Mon, Jan 14, 2013 at 7:20 PM, James Starlight
> wrote:
>
>> 1)As I understood
:
>
>
> 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 sug
Cheers,
>
> --
> Szilárd
>
>
> On Thu, Jan 24, 2013 at 3:48 PM, Szilárd Páll wrote:
>
>> On Thu, Jan 24, 2013 at 3:28 PM, Justin Lemkul wrote:
>>
>>>
>>>
>>> On 1/24/13 9:23 AM, James Starlight wrote:
>>>
>>>> oh t
shots not from
x-ray structures)
How it could be fixed ?
2013/1/24 Justin Lemkul :
>
>
> 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 r
.
Using 1 MPI 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
201
t;>>> From: Szil?rd P?ll
>>>> Subject: Re: [gmx-users] Problem with gromacs-4.6 compilation on
>>>> Debian
>>>> To: Discussion list for GROMACS users
>>>> Message-ID:
>>>> >>> gmail.com <3yncu1aegv7hcac
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 g_Co
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
ames
2013/1/22 Szilárd Páll :
> On Tue, Jan 22, 2013 at 12:45 PM, James Starlight
> wrote:
>
>> 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&
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 :
> Szilárd
--
gmx-users mailing listgmx-users@gromacs.org
http:
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 :
> Thank you!
>
&g
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
2
Lemkul :
>
>
> 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
avoid it ?
2013/1/17 James Starlight :
> 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 se
2013 at 1:51 PM, James Starlight
> 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 consequentl
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 some
must to
increase c12 or decreace C6 terms. Does it correct in general ?
2013/1/17 Bogdan Costescu :
> On Thu, Jan 17, 2013 at 10:59 AM, James Starlight
> wrote:
>> thank you for so detailed explanation.
>
> You're welcome. Now it's up to you to use it :)
>
>> No
les) ?
James
2013/1/6 Bogdan Costescu :
> On Sun, Jan 6, 2013 at 1:44 PM, James Starlight
> 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'
Note that we're doing a major rework of the code base to C++ in the next
>>> year (or more), so people implementing new features may wish to consider
>>> that in their choice to write code :-)
>>>
>>> Mark
>>>
>>> On Tue, Jan 15, 2013 at 2:26 P
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 Pá
ns of WHAM
method).
James
2013/1/15 James Starlight :
> 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 s
Justin, thanks both options works perfect.
James
2013/1/15 Justin Lemkul :
>
>
> 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
1 - 100 of 438 matches
Mail list logo
