An update to anyone interested:
Regenerating velocities by itself did not solve the problem. I had to
regenerate velocities and couple the upper and lower leaflets separately to
the thermostat to equilibrate the system. To smoothen the equilibration
process further, I used a 0.5 fs timestep instead
Hi Tsjerk,
That was very sage advice! Thank you. I will try regenerating velocities
and see if the motion goes away...
On Wed, Nov 13, 2013 at 2:00 PM, Tsjerk Wassenaar wrote:
> Hi Rajat,
>
> If you remove comm on the bilayer, there may be relative comm between
> leaflets. If that relative moti
Hi Rajat,
If you remove comm on the bilayer, there may be relative comm between
leaflets. If that relative motion is significant and you switch to removing
comm per leaflet, the program suddenly finds itself resetting the com over
a large distance. About equilibration, you equilibrated with comm_g
On 11/12/13 1:47 PM, Rama wrote:
Hi Justin,
Below I pasted .mdp file and topology. In .log file I could see energy term
for position restraints.
.mdp file---
title = NPT Equilibration
define = -DPOSRES ; position restraints for protein
; Run paramet
rpose when cutoff >1.6 but the
total performance (ns/day) decreases severely. That's NOT what I want
because I would like to assign 0.8 or 1.0 or 1.2 nm to cutoffs for general
purposes. In this tested case, I am testing Justin's umbrella's pull-code
in his tutorial.
I should a
On 11/12/13 12:14 PM, cjalmeciga wrote:
The output of energy minimization was
Potential Energy = -1.42173622068236e+06
Maximum force = 9.00312066109319e+02 on atom 148
Norm of force = 2.06087515037187e+01
OK, reasonable enough. How about a description of what the system is, whi
On 11/12/13 12:07 PM, arunjones wrote:
Thank you Sir,
initially i was running on 60 threads, now i changed it to 100. simulation
is running with out any error, but i found a note in the log file as fallows
#nodes mismatch,
current program: 100
checkpoint file: 60
#PME-nodes mi
On 11/12/13 11:10 AM, arunjones wrote:
Hello Sir,
Thanks for the reply.
now is it fine if i use 100 threads in my restart.
is there any impact on the over all simulation?
Only if that is the number of threads originally used in the run. If not, there
will be a mismatch between the DD grid
On 11/12/13 10:58 AM, cjalmeciga wrote:
I run
grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
and everything looks fine. I check the nvt.tpr, and temperature is ok.
The fact that grompp completes indicates there is nothing syntactically wrong
with the input files. Whethe
24 10025398.693 173338.93624.1
> PME 3D-FFT 24 10022798.48289852.482 12.5
> PME 3D-FFT Comm. 24 1002 947.03330406.937 4.2
> PME solve 24501 420.66713506.611 1.9
> -
On 11/12/13 8:33 AM, bharat gupta wrote:
Thanks justin for your replies. I understood the g_analyze related data. I
tired g_analyze to dump the structures as you said. But, I didn't find any
switch that can be used to dump the structure in pdb format.
Because that's not the function of g_ana
Thanks justin for your replies. I understood the g_analyze related data. I
tired g_analyze to dump the structures as you said. But, I didn't find any
switch that can be used to dump the structure in pdb format.
On Tue, Nov 12, 2013 at 10:15 PM, Justin Lemkul wrote:
>
>
> On 11/11/13 6:56 PM, bh
On 11/11/13 6:56 PM, bharat gupta wrote:
Hi,
I tried g_select to dump the structure with the interacting water
molecules, but I don't know know how to do that. I searched for some
threads in the discussion but wasn't able to find anything related to my
need. Can you explain how can I do that ?
On 11/11/13 5:39 PM, bharat gupta wrote:
Sorry, I attached the wrong file . Here's the average file generate from
one of the files I sent in my last mail. I used the command g_analyze -f
hbond_115-water.xvg -av hbond_115-water-avg.xvg. Here's the file obtained
from this command :-
https://www.
There are no problems to have ions while using Reaction-Field treatment.
Dr. Vitaly V. Chaban
On Mon, Nov 11, 2013 at 7:06 PM, Justin Lemkul wrote:
>
>
> On 11/11/13 12:08 PM, Williams Ernesto Miranda Delgado wrote:
>>
>> Hello
>> If I did the MD simulation using PME and neutralized with ions,
On 11/11/13 12:08 PM, Williams Ernesto Miranda Delgado wrote:
Hello
If I did the MD simulation using PME and neutralized with ions, and I want
to rerun this time with reaction field zero, is there any problem if I
keep the ions? This is for LIE calculation. I am using AMBER99SB.
Why do you th
Hi,
I tried g_select to dump the structure with the interacting water
molecules, but I don't know know how to do that. I searched for some
threads in the discussion but wasn't able to find anything related to my
need. Can you explain how can I do that ?
On Tue, Nov 12, 2013 at 7:39 AM, bharat gu
Sorry, I attached the wrong file . Here's the average file generate from
one of the files I sent in my last mail. I used the command g_analyze -f
hbond_115-water.xvg -av hbond_115-water-avg.xvg. Here's the file obtained
from this command :-
https://www.dropbox.com/s/sovzk40cudznfjw/hbond_115-water
On 11/11/13 4:06 AM, bharat gupta wrote:
In addition to my previous question, I have another question about
g_analyze. When I used the hbond.xvg file to get the average and plotted
the average.xvg file I found that the average value is round 4 to 5
according to the graph. But g_analyze in its f
On 11/11/13 1:30 AM, bharat gupta wrote:
thank you informing about g_rdf...
Is it possible to dump the structure with those average water molecules
interacting with the residues. I generated the hbond.log file which gives
the details but I need to generate a figure for this ??
g_select
-Ju
In addition to my previous question, I have another question about
g_analyze. When I used the hbond.xvg file to get the average and plotted
the average.xvg file I found that the average value is round 4 to 5
according to the graph. But g_analyze in its final calculation gives 7.150
as the average v
thank you informing about g_rdf...
Is it possible to dump the structure with those average water molecules
interacting with the residues. I generated the hbond.log file which gives
the details but I need to generate a figure for this ??
On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul wrote:
>
On 11/10/13 8:38 PM, bharat gupta wrote:
But trjorder can be used to calculate the hydration layer or shell around
residues ... Right ??
Yes, but I also tend to think that integrating an RDF is also a more
straightforward way of doing that. With trjorder, you set some arbitrary cutoff
tha
But trjorder can be used to calculate the hydration layer or shell around
residues ... Right ??
On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul wrote:
>
>
> On 11/10/13 8:30 PM, bharat gupta wrote:
>
>> Thanks for your reply. I was missing the scientific notation part. Now
>> everything is fine
On 11/10/13 8:30 PM, bharat gupta wrote:
Thanks for your reply. I was missing the scientific notation part. Now
everything is fine.
Regarding trjorder, it doesn't measure h-bonds but gives the water nearest
to protein.
I wouldn't try to draw any sort of comparison between the output of trjo
Thanks for your reply. I was missing the scientific notation part. Now
everything is fine.
Regarding trjorder, it doesn't measure h-bonds but gives the water nearest
to protein.
On Mon, Nov 11, 2013 at 10:12 AM, Justin Lemkul wrote:
>
>
> On 11/10/13 7:18 PM, bharat gupta wrote:
>
>> I check
On 11/10/13 7:18 PM, bharat gupta wrote:
I checked the file hbnum.xvg file and it contains three columns - time,
hbonds, hbonds that donot follow the angle criteria. In that case SS1 is
The third column is not actually H-bonds, then ;)
the average of actual hbonds (2nd column ) and SS2 is t
I checked the file hbnum.xvg file and it contains three columns - time,
hbonds, hbonds that donot follow the angle criteria. In that case SS1 is
the average of actual hbonds (2nd column ) and SS2 is the average of 3rd
column. Am I right here or not ??
I tried to calculate the h-bond for residues 1
On 11/10/13 12:20 AM, bharat gupta wrote:
Hi,
I used the command g_hbond to find h-bond between residues 115-118 and
water. Then I used g_analyze to find out the average and it gives the value
for the hbonds like this :-
std. dev.relative deviation of
t it. To hope to see some
scaling, you'd need to be able to drop the PME mesh time by about a factor
of two (coarser grid, and compensating increase to rcoulomb), and hope
there was enough PP work that using two GPUs for a single simulation is
even worth considering. Achieving throughput-style scal
Time: 178961.45022398.880 799.0
6h13:18
(ns/day)(hour/ns)
Performance: 38.5730.622
--
View this message in context:
http://gromacs.5086.x6.nabble.com/mdrun-on-8-core-AMD-GTX-TITAN-was-Re-gmx-users-Re-Gromacs-4-6-on-t
On 11/9/13 9:51 PM, Gianluca Interlandi wrote:
On Sat, 9 Nov 2013, Gianluca Interlandi wrote:
Just to chime in. Here is a that paper might be helpful in understanding the
role of cuoffs in the CHARMM force field:
AU STEINBACH, PJ
BROOKS, BR
AF STEINBACH, PJ
BROOKS, BR
TI NEW SPHERICAL
On 11/9/13 4:16 PM, rajat desikan wrote:
Hi Justin,
I take it that both the sets of parameters should produce identical
macroscopic quantities.
For the GPU, is this a decent .mdp?
cutoff-scheme= Verlet
vdwtype = switch
rlist= 1.2
;rlistlong = 1.4
On 11/8/13 3:32 PM, Williams Ernesto Miranda Delgado wrote:
Greetings again
If I use a salt concentration for neutralizing the protein-ligand complex
and run MD using PME, and the ligand is neutral, do I perform ligand MD
simulation without adding any salt concentration? It could be relevant fo
On 11/9/13 12:48 AM, pratibha wrote:
Sorry for the previous mistake. Instead of 53a7, the force field which I
used was 53a6.
53A6 is known to under-stabilize helices, so if a helix did not appear in a
simulation using this force field, it is not definitive proof that the structure
does no
On 11/7/13 11:32 PM, Rajat Desikan wrote:
Dear All,
The setting that I mentioned above are from Klauda et al., for a POPE
membrane system. They can be found in charmm_npt.mdp in lipidbook (link
below)
http://lipidbook.bioch.ox.ac.uk/package/show/id/48.html
Is there any reason not to use their
I'd at least use RF! Use a cut-off consistent with the force field
parameterization. And hope the LIE correlates with reality!
Mark
On Nov 7, 2013 10:39 PM, "Williams Ernesto Miranda Delgado" <
wmira...@fbio.uh.cu> wrote:
> Thank you Mark
> What do you think about making a rerun on the trajectori
On Thu, Nov 7, 2013 at 6:34 AM, James Starlight wrote:
> 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 b
Let's not hijack James' thread as your hardware is different from his.
On Tue, Nov 5, 2013 at 11:00 PM, Dwey Kauffman wrote:
> Hi Szilard,
>
>Thanks for your suggestions. I am indeed aware of this page. In a 8-core
> AMD with 1GPU, I am very happy about its performance. See below. My
Actual
Hi Mark!
I think that this is the paper that you are referring to:
dx.doi.org/10.1021/ct900549r
Also for your reference, these are the settings that Justin recommended
using with CHARMM in gromacs:
vdwtype = switch
rlist = 1.2
rlistlong = 1.4
rvdw = 1.2
rvdw-switch = 1.0
rcoulomb = 1.2
As y
If the long-range component of your electrostatics model is not
decomposable by group (which it isn't), then you can't use that with LIE.
See the hundreds of past threads on this topic :-)
Mark
On Thu, Nov 7, 2013 at 8:34 PM, Williams Ernesto Miranda Delgado <
wmira...@fbio.uh.cu> wrote:
> Hell
Reasonable, but CPU-only is not 100% conforming either; IIRC the CHARMM
switch differs from the GROMACS switch (Justin linked a paper here with the
CHARMM switch description a month or so back, but I don't have that link to
hand).
Mark
On Thu, Nov 7, 2013 at 8:45 PM, rajat desikan wrote:
> Than
Thank you, Mark. I think that running it on CPUs is a safer choice at
present.
On Thu, Nov 7, 2013 at 9:41 PM, Mark Abraham wrote:
> Hi,
>
> It's not easy to be explicit. CHARMM wasn't parameterized with PME, so the
> original paper's coulomb settings can be taken with a grain of salt for use
>
On 11/7/13 12:14 PM, pratibha wrote:
My protein contains metal ions which are parameterized only in gromos force
field. Since I am a newbie to MD simulations, it would be difficult for me
to parameterize those myself.
Can you please guide me as per my previous mail which out of the two
simulat
Hi,
It's not easy to be explicit. CHARMM wasn't parameterized with PME, so the
original paper's coulomb settings can be taken with a grain of salt for use
with PME - others' success in practice should be a guideline here. The good
news is that the default GROMACS PME settings are pretty good for a
On Wed, Nov 6, 2013 at 4:07 PM, fantasticqhl wrote:
> Dear Justin,
>
> I am sorry for the late reply. I still can't figure it out.
>
It isn't rocket science - your two .mdp files describe totally different
model physics. To compare things, change as few things as necessary to
generate the compar
First, there is no value in ascribing problems to the hardware if the
simulation setup is not yet balanced, or not large enough to provide enough
atoms and long enough rlist to saturate the GPUs, etc. Look at the log
files and see what complaints mdrun makes about things like PME load
balance, and
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
On 11/5/13 7:14 PM, Stephanie Teich-McGoldrick wrote:
Message: 5
Date: Mon, 04 Nov 2013 13:32:52 -0500
From: Justin Lemkul
Subject: Re: [gmx-users] Analysis tools and triclinic boxes
To: Discussion list for GROMACS users
Message-ID: <5277e854.9000...@vt.edu>
Content-Type: text/plain; charset=
Hi Dwey,
On 05/11/13 22:00, Dwey Kauffman wrote:
Hi Szilard,
Thanks for your suggestions. I am indeed aware of this page. In a 8-core
AMD with 1GPU, I am very happy about its performance. See below. My
intention is to obtain a even better one because we have multiple nodes.
### 8 core AMD
Yes, that has been true for GROMACS for a few years. Low-latency
communication is essential if you want a whole MD step to happen in around
1ms wall time.
Mark
On Nov 5, 2013 11:24 PM, "Dwey Kauffman" wrote:
> Hi Szilard,
>
> Thanks.
>
> >From Timo's benchmark,
> 1 node142 ns/day
> 2
f Michael Shirts
> Sent: Thursday, 31 October 2013 1:52 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] RE: Gibbs Energy Calculation and charges
>
> I likely won't have much time to look at it tonight, but you can see
> exactly what the option is doing to t
On Tue, Nov 5, 2013 at 9:55 PM, Dwey Kauffman wrote:
> Hi Timo,
>
> Can you provide a benchmark with "1" Xeon E5-2680 with "1" Nvidia
> k20x GPGPU on the same test of 29420 atoms ?
>
> Are these two GPU cards (within the same node) connected by a SLI (Scalable
> Link Interface) ?
Note that
Hi Dwey,
First and foremost, make sure to read the
http://www.gromacs.org/Documentation/Acceleration_and_parallelization
page, in particular the "Multiple MPI ranks per GPU" section which
applies in your case.
Secondly, please do post log files (pastebin is your friend), the
performance table at
Timo,
Have you used the default settings, that is one rank/GPU? If that is
the case, you may want to try using multiple ranks per GPU, this can
often help when you have >4-6 cores/GPU. Separate PME ranks are not
switched on by default with GPUs, have you tried using any?
Cheers,
--
Szilárd Páll
You need to configure your MPI environment to do so (so read its docs).
GROMACS can only do whatever that makes available.
Mark
On Tue, Nov 5, 2013 at 2:16 AM, bharat gupta wrote:
> Hi,
>
> I have installed Gromcas 4.5.6 on Rocks cluster 6.0 andmy systme is having
> 32 processors (cpu). But whi
On 11/5/13 10:34 AM, J Alizadeh wrote:
Hi,
I need to replace an atom with another in the considered system.
I'd like to know if it is possible and if so what changes I need to do.
The coordinate file replacement is trivial. Just open the file in a text editor
and repname the atom. The top
29420 Atoms with a some tuning of the write out and communication intervals:
nodes again: 2 x Xeon E5-2680v2 + 2 x NVIDIA K20X GPGPUs @ 4fs vsites
1 node 212 ns/day
2 nodes 295 ns/day
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gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please
On 11/5/13 7:19 AM, Kalyanashis wrote:
I have given my .mdp file,
; title = trp_drg
warning = 10
cpp = /usr/bin/cpp
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps
On Mon, Nov 4, 2013 at 12:01 PM, bharat gupta wrote:
> Hi,
>
> I am trying to install gromacs 4.5.7 on rocks cluster(6.0) and it works
> fine till .configure command, but I am getting error at the make command :-
>
> Error:
>
> [root@cluster gromacs-4.5.7]# make
>
These is no
Brad,
These numbers seems rather low for a standard simulation setup! Did
you use a particularly long cut-off or short time-step?
Cheers,
--
Szilárd Páll
On Fri, Nov 1, 2013 at 6:30 PM, Brad Van Oosten wrote:
> Im not sure on the prices of these systems any more, they are getting dated
> so th
just a small benchmark...
each node - 2 x Xeon E5-2680v2 + 2 x NVIDIA K20X GPGPUs
42827 atoms - vsites - 4fs
1 node142 ns/day 2 nodes FDR14 218 ns/day
4 nodes FDR14 257 ns/day
8 nodes FDR14 326 ns/day
16 nodes FDR14 391 ns/day (global warming)
best,
timo
--
gmx-users mailing list
On 11/3/13 7:12 AM, rankinb wrote:
That last procedure works. I really appreciate your help. The only other
question I have is related to the selection process. Is there a way to
select the oxygen atoms of water within a certain distance of a molecule, as
well as the corresponding hydrogen a
On 11/2/13 12:25 PM, rankinb wrote:
Here are the steps that I used:
1. trjconv -pbc whole -dump 37.875
2. trjconv -pbc nojump
3. trjconv -center
4. g_select to make an index containing the atoms of interest
5. trjconv to extract coordinates
Regardless of whether step 1 is used or not, th
On 11/2/13 11:23 AM, rankinb wrote:
Tsjerk,
Thanks for your reply. I have tried using the center option, but ran into
similar problems. Here are the exact commands that I used:
g_select -f file.xtc -s file.tpr -n index.ndx -select 'group 14 and within
0.71 of group 13' -b 37.875 -e 37.875 -
On 11/2/13 6:32 AM, Hossein Lanjanian wrote:
Thank Justin for your help
What forcefield is most suitable to study this case?
The one that your careful study of the literature tells you is the most
reliable. It's up to you to justify your choice, not what someone on the
Internet tells you :
I think ProDy can do this. It is a python module for analysis of
structures that can be downloaded from http://www.csb.pitt.edu/ProDy/
I'm not sure it can read xtc but you can probably use it after converting
trajectories to pdb.
>> On 10/30/13 11:26 AM, Knapp Bernhard wrote:
>>> Hi users,
>>>
>>>
On 10/31/13 4:57 AM, fantasticqhl wrote:
Dear Justin,
*Thanks very much for your reply! Here is my minim.mdp I used:*
/; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (ste
I likely won't have much time to look at it tonight, but you can see
exactly what the option is doing to the topology. run gmxdump on the
tpr. All of the stuff that couple-intramol does is in grompp, so the
results will show up in the detailed listings of the interactions, and
which ones have whi
Michael, thanks for taking the time to comment and have a look.
The real issue I am having is a bit deeper into the topic than that, my last
reply was just an observation on something else. Will summarise what I have
been doing etc.
I have a molecule that are calculating the Gibbs energy of hy
I think the grammar got a little garbled there, so I'm not sure quite
what you are claiming.
One important thing to remember; 1-4 interactions are treated as
bonded interactions right now FOR COUPLE intramol (not for lambda
dependence of the potential energy function), so whether
couple-intramol i
On 10/28/13 8:07 PM, Hari Pandey wrote:
Many thanks to Dr.Lemkul
Yes mass is 444 in my .top file and I did "-density 1000 " because then it
will show the density also.
If you have one molecule in a box of a known size, you don't need any
command-line flags - you have a mass and a known
Many thanks to Dr.Lemkul
Yes mass is 444 in my .top file and I did "-density 1000 " because then it
will show the density also.
I am wandering how do I find that which atom name mismatched. The
forcefield folder is in my working directory and there are all files.
atomtypes.atp is there
On 10/28/13 7:41 PM, Hari Pandey wrote:
Thank you so much Mark.
I still did not understand. More detaily. Atomtypes are only following:
atomtypes.atp::
H 1.00800 ; polar H
DUM0.0 ; dummy atom
HAL1 1.008000 ; alphatic proton
HAL2 1.008000 ;
Thank you so much Mark.
I still did not understand. More detaily. Atomtypes are only following:
atomtypes.atp::
H 1.00800 ; polar H
DUM 0.0 ; dummy atom
HAL1 1.008000 ; alphatic proton
HAL2 1.008000 ; alphatic proton
HAL3 1.008000 ;
On Mon, Oct 28, 2013 at 8:04 PM, Hari Pandey wrote:
> Dear Gromacs Users,
>
> First, I would like to thank Dr. Lemkul for reply.
>
> My problem description is as follows:
> I am using CHARMM36 forcefield to equilibrate of AOT. when I add the mass
> of all atoms from topology, it gives me 444.5 w
On Sat, Oct 26, 2013 at 2:07 PM, Santu Biswas wrote:
> >
> >
> >
> > "Not working" is too vague a symptom for anyone to guess what the problem
> > is, sorry.
> >
> > Mark
> > On Oct 24, 2013 9:39 AM, "Santu Biswas"
> wrote:
> >
> > > dear users,
> > >
> > > I am performing 500ps mdr
Hi Kevin,
Thanks.
Houyang
On Thu, Oct 24, 2013 at 3:00 PM, sri2201 wrote:
> Hi
> I would like to try it out
>
> Srinivasa Rao Penumutchu
> Research Scholar
> Protein NMR Lab , II floor-218
> Department of Chemistry
> National Tsing Hua University,
> Hsinchu, Taiwan.
> Ph: 886357151-35605,
> Emai
On Thu, Oct 24, 2013 at 6:24 PM, Corina Mo wrote:
> Dear Justin,
>
> Thanks again! Will look into it.
> Btw, you know if there is any plan to implement implicit lipid model in
> GROMACS?
>
No plans known.
Mark
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gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/
Hi,
I also want to try :)
Best regards,
~Thu
On Wed, Oct 23, 2013 at 11:39 PM, houyang chen wrote:
> Hi Kevin
> Can I have a try?
> Best
> Houyang
>
>
> On Wed, Oct 23, 2013 at 12:30 PM, Villarealed wrote:
>
> > Sound nice. I would like to try out.
> > Could You please set up an account for me
Hi Kevin
Can I have a try?
Best
Houyang
On Wed, Oct 23, 2013 at 12:30 PM, Villarealed wrote:
> Sound nice. I would like to try out.
> Could You please set up an account for me?
> Regards,
> Eduardo Villarreal
> villarea...@hss.edu
>
> -
> Eduardo Villarreal Ramírez
> Postdoctoral Research F
Hi!
It is strange but such combination works:
CC=icc CXX=icpc ~/cmake-2.8.12/bin/cmake ..
-DCMAKE_INSTALL_PREFIX=/ifs/apps/GROMACS-4.6.3 -DGMX_X11=OFF
-DGMX_MPI=ON -DGMX_FFT_LIBRARY=mkl -DGMX_GPU=ON >&cmake.log
It was a command that our cluster administrator was able to configure
GROMACS wi
On 10/19/13 11:53 AM, Sathya wrote:
Dear Justin,
Please Tell me is there any possible option for inserting cr into into DPPC
bilayer.
Well, anything is possible. You'd have to define an atomtype that represents
Cr, which will involve deriving suitable LJ parameters that reproduce some
ex
Hello, Mark!
16.10.2013 18:17, Mark Abraham wrote:
On Wed, Oct 16, 2013 at 12:27 PM, Nikolay Alemasov wrote:
Thank you, Mark!
It was already tried. I mean a fresh unpacking and further cmake run.
As for your first thought concerning a loss of access to some parts of
gmxlib:
[alemasov@
On Wed, Oct 16, 2013 at 12:27 PM, Nikolay Alemasov wrote:
> Thank you, Mark!
>
> It was already tried. I mean a fresh unpacking and further cmake run.
> As for your first thought concerning a loss of access to some parts of
> gmxlib:
>
>> [alemasov@nks-g6 gromacs-4.6.3]$ ls -l ./src/gmxlib/ |
On 10/9/13 11:28 AM, ABEL Stephane 175950 wrote:
Hello Justin,
Two quick questions, here
- Since the lipid charmm36 parameters for lipids are already available in the
gromacs format on the GROMACS website (charmm36.ff_4.5.4_ref.tgz) from thomas
Piggot. Does it means that these files are co
First I created index file with all oxygen atoms of water molecules using
make_ndx -f lys_full.gro -o index_soloxy.ndx
Then I used g_hydorder -f lys_full.xtc -s lys_full.tpr -n index_soloxy.ndx
-or file1.out file2.out
Following output appeared:
Program g_hydorder, VERSION 4.6.3
Source code file: /
You need to contact your cluster administrator for instructions of how to
submit jobs to the cluster. Usually you have to create some kind of
shell-script that specifies various parameters of your job and then submit it
to a queue system.
Below you submitted the job most likely to the 'head-nod
Hmm. This really isn't quite enough information to go on. Can you
file a redmine issue, and include the files used to generate the run
that crashed (.mdp, .gro,. .top), as well as the files that show it
failing (.log)?
http://redmine.gromacs.org/
On Thu, Oct 3, 2013 at 4:32 AM, Jernej Zidar wro
On 2013-10-01 19:51, Nidhi Katyal wrote:
Please provide me with necessary guidance. I have already posted this
thrice but have not got a single reply
Thanks in advance.
On Tue, Oct 1, 2013 at 3:40 PM, Nidhi Katyal wrote:
Hello everyone,
I would like to calculate angle tetrahedral order param
On 9/27/13 8:18 AM, Anna Marabotti wrote:
Dear Justin,
sorry for the late answer and acknowledgements... Please see below my
comments.
Anna
__
Anna Marabotti, Ph.D.
Assistant Professor
Department of Chemistry and Biology
University of Salerno
Via G
If diff says there are no changes, then you're not comparing with the file
you changed...
On Sep 25, 2013 1:59 PM, "shahab shariati"
wrote:
> Dear Mark
>
> > The UNIX tool diff is your friend for comparing files.
>
> Thanks for your suggestion. I used diff and sdiff toll
> for comparing 2 files (
I found this list useful:
http://md.chem.rug.nl/cgmartini/index.php/blog/265-comparingforcefields
http://md.chem.rug.nl/cgmartini/index.php/blog/269-jungle2
On Wed, Sep 25, 2013 at 4:16 PM, fcarb wrote:
> If it may be of help this paper
> (
> http://www.ncbi.nlm.nih.gov/pubmed/?term=Systematic+
On 9/23/13 11:43 PM, Santhosh Kumar Nagarajan wrote:
Justin..
I understand the problem..
But.. How to generate a .rtp file myself..
Study existing examples, read manual section 5.6.1, and fire up a text editor.
-Justin
--
==
Justin A. Lemkul
On 9/23/13 4:04 PM, akk5r wrote:
With what was said: what do you all think of the following parameters for
Charmm 36:
rlist = 1.2
rlistlong = 1.4
vdwtype = cutoff
rvdw-switch = 1.0
rvdw = 1.2
rcouloumb = 1.2
vdw-modifier = Potential-shift-Verlet
DispCorr = No
cutoff-scheme = Verlet
rvdw-swi
On 9/20/13 7:59 AM, Mark Abraham wrote:
Note that the group scheme does not reproduce the (AFAIK unpublished)
CHARMM switching scheme, either.
In case anyone is interested, the reference cited in the CHARMM papers for the
switching and shifting functions is dx.doi.org/10.1002/jcc.540150702.
On Mon, Sep 23, 2013 at 2:40 PM, Jong Wha Lee wrote:
> Dear Vitaly,
>
>
>
> Thank you for your suggestion.
>
>
>
> I have also tried calculating interaction energies by specifying energygrps
> in .mdp file, but calculated energies deviate greatly from QM calculated
> energies and experimental resu
On 9/23/13 3:28 AM, Jonathan Saboury wrote:
That said, there is an spc.itp within the AMBER subdirectories that needs
to be
#included more explicitly, i.e. #include "amber99sb.ff/spc.itp"
May I ask why you are using SPC? The AMBER force fields were parametrized
with
TIP3P, so I see no via
On 9/22/13 10:10 PM, Jonathan Saboury wrote:
Then something is wrong with the way you've done it, because the job of
spc.itp
is to define the [moleculetype] SOL and all its relevant parameters.
Hm...not sure what the matter is. Added a forcefield as well as spc.itp to
the .top file made by
On 9/21/13 5:15 PM, Jonathan Saboury wrote:
Have a look at how Justin's tutorial's .top gets access to a water
topology.
Mark
Thank you very much for the response Mark!
I've looked at his .top and it seems to me that how he included it is by
adding "#include spc.itp". I've added that line
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