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 jalem...@vt.edu wrote:
On 11/10/13 7:18 PM, bharat gupta 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.
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
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 jalem...@vt.edu wrote:
On 11/10/13 8:30 PM, bharat gupta wrote:
Thanks for your reply. I was missing the scientific notation part. Now
everything
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
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
Dear Kieu Thu
Thanks for your comment about free energy. Unfortunately, I could not send a
email to Paissoni Cristina in the Gromacs Forum.
Could you give me email address of Paissoni Cristina? Finding a tool for
calculation MM/PBSA with Gromacs is very vital for me.
Best Regards
Kiana
--
Dear users,
I am investigating protein crystal packing artifacts by doing equilibrium
simulations starting from a crystal structure. I would like to know if the
relaxations i see are reproducible, in the sense that many simulations with
independent velocities give the same general result.
My
Hi All,
I have a few older membrane simulations for which the COM for the upper and
lower leaflets were not removed in the course of the simulations. These are
pretty long simulations exceeding 300 ns.
I have trouble with post-processing of the trajectory.
To remove the COM of the upper and lower
Daer Justin
I studied your tutorial (Umbrella Sampling). It is very beneficial for me.
The system you considered was the dissociation of a single peptide from the
growing end of an protofibril.
You considered following parameters:
Chain_B: reference group for pulling.
Chain_A: group to which
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
On 11/9/13 5:24 AM, rajat desikan wrote:
Hi All,
I have a few older membrane simulations for which the COM for the upper and
lower leaflets were not removed in the course of the simulations. These are
pretty long simulations exceeding 300 ns.
I have trouble with post-processing of the
On 11/9/13 8:22 AM, shahab shariati wrote:
Daer Justin
I studied your tutorial (Umbrella Sampling). It is very beneficial for me.
The system you considered was the dissociation of a single peptide from the
growing end of an protofibril.
You considered following parameters:
Chain_B:
On 11/8/13 2:27 PM, Williams Ernesto Miranda Delgado wrote:
Greetings
The discussion list had helped me about understanding what to do when I
want to calculate binding free energy using LIE after doing MD simulation
using PME.
Now I need your help about choosing the simulation box size for
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
Dear Justin
Thanks for your explanation.
My system contains lipid bilayer + drug + water molecules.
I want to calculate Potential of mean force as a function of the distance
between the centers of mass of drug and the lipid bilayer.
Box vector along which the pulling is being conducted is Z.
On 11/9/13 9:38 AM, shahab shariati wrote:
Dear Justin
Thanks for your explanation.
My system contains lipid bilayer + drug + water molecules.
I want to calculate Potential of mean force as a function of the distance
between the centers of mass of drug and the lipid bilayer.
Box vector
Hi Justin,
1) I am doing all three. -type x, -type y, -lateral z (xy) ...(I am looking
at anisotropy in dynamics if any)
2) Yes, 192 phosphate beads is exact. I have 384 lipids in my system
(192/leaflet)
If you were to remove the COM motion of individual leaflets and extract the
MSD, what would
On 11/9/13 11:37 AM, rajat desikan wrote:
Hi Justin,
1) I am doing all three. -type x, -type y, -lateral z (xy) ...(I am looking
at anisotropy in dynamics if any)
2) Yes, 192 phosphate beads is exact. I have 384 lipids in my system
(192/leaflet)
If you were to remove the COM motion of
Hi Justin,
Thanks for your time. I think I will use g_traj to spit out the P8
coordinates from upperP8_center_pbcnojump.xtc and write my own little MSD
routine :)
On Sat, Nov 9, 2013 at 11:36 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/9/13 11:37 AM, rajat desikan wrote:
Hi Justin,
1)
On Sat, Nov 9, 2013 at 9:36 AM, alex.bjorling alex.bjorl...@gmail.comwrote:
Dear users,
I am investigating protein crystal packing artifacts by doing equilibrium
simulations starting from a crystal structure. I would like to know if the
relaxations i see are reproducible, in the sense that
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 NOT USED IN GPU...IS
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 =
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-CUTOFF METHODS FOR LONG-RANGE FORCES IN
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
Hi Szilard,
Thank you very much for your suggestions.
Actually, I was jumping to conclusions too early, as you mentioned AMD
cluster, I assumed you must have 12-16-core Opteron CPUs. If you
have an 8-core (desktop?) AMD CPU, than you may not need to run more
than one rank per GPU.
Yes, we do
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
standard -
Dear Justin and Mark Thank you for your Previous reply
Can i Use the Following Intel Compiler for grmacs 4.6.2 in
centos Linux OS ?
Intel® C++ Composer XE 2013 for Linux
it Includes Intel® C++ Compiler, Intel® Integrated Performance Primitives 7.1,
Intel® Math Kernel
Dear Changwoon,
why are you using ./make_ndx instead of make_ndx? Did you try to use the
command without ./?
Regards
El jue, 07-11-2013 a las 14:12 -0800, Chang Woon Jang escribió:
Dear Users,
I am using openSUSE 12.3 and try to use make_ndx and g_angle. When I try
the following
Hi, this feature is really really experimental and should indeed be
avoided. If opls you want, then give a try with
http://www.aribeiro.net.br/mktop/
Alan
On 8 November 2013 04:42, aditya sarma adityasrm...@gmail.com wrote:
Hi,
i was trying to generate topology for p-phenylene vinylene
Should I start with helical peptides and see if it maintains the helicity
or I can start with random coil?
Do random coil peptides take long simulation time to form helical peptides?
any help on this will be appreciated.
On Tue, Nov 5, 2013 at 12:25 AM, Archana Sonawani-Jagtap
Hello again,
That depends on the peptide. There is no general answer. I am starting with
a linear conformations, but that's because I'm working with intrinsically
disordered proteins. That's as far as I can go regarding telling you about
what I'm doing. I'm not at liberty to discuss these things,
Hi,
That shouldn't happen if your MPI library is working (have you tested it
with other programs?) and configured properly. It's possible this is a
known bug, so please let us know if you can reproduce it in the latest
releases.
Mark
On Fri, Nov 8, 2013 at 6:55 AM, Qin Qiao qiaoqi...@gmail.com
On Fri, Nov 8, 2013 at 12:02 AM, Jones de Andrade johanne...@gmail.comwrote:
Really?
Of course. With openmp gets to use all your cores for PME+bondeds+stuff
while the GPU does PP. Any version without openmp gets to use one core per
domain, which is bad.
An what about gcc+mpi? should I
Ok, you convinced me. I'll really give it a try. I'm following this throw
the suposition that openMP implementation on intel compilers is not as good
as GNU compilers. I already tested intel openMP in our cluster, and it just
sucked in comparison to the pure MPI compilation.
Let's hope I can make
Dear Justin Thank you for your Previous reply,
I am trying to Install gromacs 4.6.2 in a cluster having centos
OS with teh Following Command I got following error
cmake ..
-DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON
-DGMX_DOUBLE=ON
CMake Warning at
On Fri, Nov 8, 2013 at 7:18 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
Hi,
That shouldn't happen if your MPI library is working (have you tested it
with other programs?) and configured properly. It's possible this is a
known bug, so please let us know if you can reproduce it in the
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
On 11/8/13 7:44 AM, vidhya sankar wrote:
Dear Justin Thank you for your Previous reply,
I am trying to Install gromacs 4.6.2 in a cluster having centos
OS with teh Following Command I got following error
cmake ..
-DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON
-DGMX_DOUBLE=ON
CMake Warning
OK, thanks.
Please open a new issue at redmine.gromacs.org, describe your observations
as above, and upload a tarball of your input files.
Mark
On Fri, Nov 8, 2013 at 2:14 PM, Qin Qiao qiaoqi...@gmail.com wrote:
On Fri, Nov 8, 2013 at 7:18 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Hi,
I have been using Gromacs for my MD liquid simulations for about 2 years
now, and, of course, it has been working great!
Now, in the current part of my project, I am looking at liquid structure,
not dynamics. Of course, one can analyze liquid structure by simply
analyzing an MD trajectory.
The only open source Monte Carlo package I have every used or now of is
MCCS Towhee:
http://towhee.sourceforge.net/
Andrew
On 11/08/2013 11:23 AM, Andrew DeYoung wrote:
Hi,
I have been using Gromacs for my MD liquid simulations for about 2 years
now, and, of course, it has been working
Dear Riccardo Concu,
The reason is that I used the make_ndx file in the working directory.
Now, I solved that problem with installing gromacs as following
cmake .. -DGMX_BUILD_OWN_FFTW=Off
Anyway, I appreciate your comment.
Best regards,
Changwoon Jang
On Friday, November 8, 2013
Dear Kieu Thu
Thanks for your comment about free energy. Unfortunately, I could not send a
email to Paissoni Cristina in the Gromacs Forum.
Could you give me email address of Paissoni Cristina? Finding a tool for
calculation MM/PBSA with Gromacs is very vital for me.
Best Regards
Kiana
--
View
Greetings
The discussion list had helped me about understanding what to do when I
want to calculate binding free energy using LIE after doing MD simulation
using PME.
Now I need your help about choosing the simulation box size for ligand and
complex. I used -d 1.0 in editconf for the complex
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 for
LIE free energy calculation if I don't include salt in ligand
Hello users
For making a rerun of a MD simulation done with PME, but this time using
Reaction field zero, do I eliminate the ions from the system, previously
added to neutralize and ran with PME? What do you think about using a
twin-range cut off instead of reaction field zero? I need to obtain
Sorry for the previous mistake. Instead of 53a7, the force field which I
used was 53a6.
On Fri, Nov 8, 2013 at 12:10 AM, Justin Lemkul [via GROMACS]
ml-node+s5086n5012325...@n6.nabble.com wrote:
On 11/7/13 12:14 PM, pratibha wrote:
My protein contains metal ions which are parameterized
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 think either is correct for practical purposes.
Mark
On Thu, Nov 7, 2013 at 8:41 AM, Gianluca Interlandi
gianl...@u.washington.edu wrote:
Does it make more sense to use nose-hoover or v-rescale when running in
implicit solvent GBSA? I understand that this might be a matter of opinion.
On Wed, Nov 6, 2013 at 4:07 PM, fantasticqhl fantastic...@gmail.com 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
Dear Sir
Presently I am working with the example file as given in the umbrella
sampling tutorial.
While running the following command
grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o npt0.tpr
I got the following error. How to debug this error.
Ignoring obsolete mdp entry
On 11/7/13 6:27 AM, Arunima Shilpi wrote:
Dear Sir
Presently I am working with the example file as given in the umbrella
sampling tutorial.
While running the following command
grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o npt0.tpr
I got the following error. How to
Dear All,
Any suggestions?
Thank you.
--
View this message in context:
http://gromacs.5086.x6.nabble.com/CHARMM-mdp-settings-for-GPU-tp5012267p5012316.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
gmx-users mailing listgmx-users@gromacs.org
Hi ALL,
Is there any way to get the percentage of each secondary structural content
of a protein using do_dssp if I supply a single PDB to it?
And how to plot the data of the -sc output from do_dssp?
Any suggestion is welcome.
Regards,
Anirban
--
gmx-users mailing listgmx-users@gromacs.org
On 11/7/13 8:24 AM, Anirban wrote:
Hi ALL,
Is there any way to get the percentage of each secondary structural content
of a protein using do_dssp if I supply a single PDB to it?
The output of scount.xvg has the percentages, but it's also trivial to do it for
one snapshot. The contents of
Hi,
I'm having trouble compiling v 4.6.3 with GPU support using CUDA 5.5.22.
The configuration runs okay and I have made sure that I have set paths
correctly.
I'm getting errors:
$ make
[ 0%] Building NVCC (Device) object
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
Dear gromacs users
I have installed gromacs 4.6.1 with cmake 2.8.12, fftw3.3.3 and openmpi-1.6.4
on a single machine with 8 cores(Red Hat Enterprise linux 6.1) . During openmpi
installation ( I used make -jN) and also in gromacs installation ( I used
make -j N command), everything seemed ok but
icc and CUDA is pretty painful. I'd suggest getting latest gcc.
Mark
On Thu, Nov 7, 2013 at 2:42 PM, ahmed.sa...@stfc.ac.uk wrote:
Hi,
I'm having trouble compiling v 4.6.3 with GPU support using CUDA 5.5.22.
The configuration runs okay and I have made sure that I have set paths
Sounds like a non-GROMACS problem. I think you should explore configuring
OpenMPI correctly, and show you can run an MPI test program successfully.
Mark
On Thu, Nov 7, 2013 at 5:51 PM, niloofar niknam
niloofae_nik...@yahoo.comwrote:
Dear gromacs users
I have installed gromacs 4.6.1 with
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
simulations should I consider more
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
Hello
I performed MD simulations of several Protein-ligand complexes and
solvated Ligands using PME for log range electrostatics. I want to
calculate the binding free energy using the LIE method, but when using
g_energy I only get Coul-SR. How can I deal with Ligand-environment long
range
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 mark.j.abra...@gmail.comwrote:
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
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
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:
Hello
Did it a few days ago. Not so much of a problem here.
But I compiled everything, including fftw, with it. The only error I got
was that I should turn off the separable compilation, and that the user
must be in the group video.
My settings are (yes, I know it should go better with openmp, but
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
You will do much better with gcc+openmp than icc-openmp!
Mark
On Thu, Nov 7, 2013 at 9:17 PM, Jones de Andrade johanne...@gmail.comwrote:
Did it a few days ago. Not so much of a problem here.
But I compiled everything, including fftw, with it. The only error I got
was that I should turn
Let's not hijack James' thread as your hardware is different from his.
On Tue, Nov 5, 2013 at 11:00 PM, Dwey Kauffman mpi...@gmail.com 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
On Thu, Nov 7, 2013 at 6:34 AM, James Starlight jmsstarli...@gmail.com 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
Thank you Mark
What do you think about making a rerun on the trajectories generated
previously with PME but this time using coulombtype: cut-off? Could you
suggest a cut off value?
Thanks again
Williams
--
gmx-users mailing listgmx-users@gromacs.org
Dear Users,
I am using openSUSE 12.3 and try to use make_ndx and g_angle. When I try
the following command, there is an error message.
./make.ndx -f data.pdb
./make_ndx: error while loading shared libraries: libcudart.so.4:cannot open
shared object file: No such file or directory
Do
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 trajectories
Really? An what about gcc+mpi? should I expect any improvement?
On Thu, Nov 7, 2013 at 6:51 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
You will do much better with gcc+openmp than icc-openmp!
Mark
On Thu, Nov 7, 2013 at 9:17 PM, Jones de Andrade johanne...@gmail.com
wrote:
Did it
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 .mdp parameters for a membrane-protein
Hi,
i was trying to generate topology for p-phenylene vinylene polymer for OPLS
forcefield using acpype . The itp file i got has the atomtype opls_x with
mass 0.00. Is there any way to rectify this?
After reading through how acpype works i found out this was one of the
possible errors but there
Dear all,
I'm trying to continue a REMD simulation using gromacs4.5.5 under NPT
ensemble, and I got the following errors when I tried to use 2 cores per
replica:
[node-ib-4.local:mpi_rank_25][error_sighandler] Caught error: Segmentation
fault (signal 11)
Dear users,
Although this topic has been extensively discussed
in the list previously, I am unclear about the solution
for the problem..
While running ligand in water simulation (EM) with RF-0
I get the following message:
Dear GMX Users,
I am wish to perform a conformational transition simulation using
coarse-grained models (SBM http://smog-server.org/). I wanted to apply flooding
to explore the conformational transition and have open-close transition my
trajectory. But what I find is that when I start from a
Dear GMX Users,
I am wish to perform a conformational transition simulation using
coarse-grained models (SBM http://smog-server.org/). I wanted to apply flooding
to explore the conformational transition and have open-close transition my
trajectory. But what I find is that when I start from a
Dear users,
Sorry for repeating the same question. I just wanted to know
whether is it ok if I have rlist rcoulomb in ligand-water and
prot-lig-water rerun md (with RF-0) while having rlist = rcoulomb
in the original simulation using PME?
Thank you
Regards
Kavya
On Wed, Nov 6, 2013 at
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
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 jalem...@vt.edu
Subject: Re: [gmx-users] Analysis tools and triclinic boxes
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 5277e854.9000...@vt.edu
On 11/6/13 5:47 AM, Kavyashree M wrote:
Dear users,
Sorry for repeating the same question. I just wanted to know
whether is it ok if I have rlist rcoulomb in ligand-water and
prot-lig-water rerun md (with RF-0) while having rlist = rcoulomb
in the original simulation using PME?
The
Thank you..
On Wed, Nov 6, 2013 at 7:39 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/6/13 5:47 AM, Kavyashree M wrote:
Dear users,
Sorry for repeating the same question. I just wanted to know
whether is it ok if I have rlist rcoulomb in ligand-water and
prot-lig-water rerun md
Hi all,
I would like to calculate the number of water molecules around any of the
methyl carbon atoms of tert-butyl alcohol. Currently, I have defined an
index group containing all three of the methyl carbon atoms and used
trjorder -nshell to calculate the number of oxygen atoms within a
I was told before I would need to use quantum calculations to do this.
What software and method would you suggest to do this?
Thanks.
-Jonathan Saboury
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gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
Hi gmx users,
I have simulated ionomer in water solution using gromos force field. But in
middle of simulation(after 2 ns) the simulation stopped and I received these
messages:
WARNING: Listed nonbonded interaction between particles 174 and 188
at distance 3f which is larger than the table
Hello
I am having trouble running a dimmer invacuo simulation. I can do energy
minimization on it, but when I attempt to generate md.tpr file I get this weird
message about “Group Protein not found in index”. I don’t see why I would need
an index file. I have no trouble generating a md.tpr
On 11/6/13 10:55 AM, rankinb wrote:
Hi all,
I would like to calculate the number of water molecules around any of the
methyl carbon atoms of tert-butyl alcohol. Currently, I have defined an
index group containing all three of the methyl carbon atoms and used
trjorder -nshell to calculate
On 11/6/13 12:53 PM, Ehsan Sadeghi wrote:
Hi gmx users,
I have simulated ionomer in water solution using gromos force field. But in
middle of simulation(after 2 ns) the simulation stopped and I received these
messages:
WARNING: Listed nonbonded interaction between particles 174 and 188
at
On 11/6/13 1:52 PM, Steve Seibold wrote:
Hello
I am having trouble running a dimmer invacuo simulation. I can do energy
minimization on it, but when I attempt to generate md.tpr file I get this
weird message about “Group Protein not found in index”. I don’t see why I
would need an index file.
Many thanks Justin. What is an appropriate cut-off value? My box size is d= 0.5
nm; based on the definition of cut-off radius, its value shouble be smaller
than d/2; therefore 0.24 is an appropriate cut-off value. Am I right?
Cheers,
Ehsan
- Original Message -
From: Justin Lemkul
On 11/6/13 2:14 PM, Ehsan Sadeghi wrote:
Many thanks Justin. What is an appropriate cut-off value? My box size is d=
0.5 nm; based on the definition of cut-off radius, its value shouble be
smaller than d/2; therefore 0.24 is an appropriate cut-off value. Am I
right?
No. The cutoff value is
What is this cut-off radius mentioned in the manual? The cut-off radius used to
truncate non-bonded inter-actions may not exceed half the shortest box vector.
Cheers,
Ehsan
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users
On 11/6/13 2:27 PM, Ehsan Sadeghi wrote:
What is this cut-off radius mentioned in the manual? The cut-off radius used
to truncate non-bonded inter-actions may not exceed half the shortest box
vector.
It refers to the longest cutoff used to evaluate nonbonded interactions,
whatever that may
Count the number of O observed near each C singly and compare the four
numbers.
Mark
On Nov 6, 2013 4:57 PM, rankinb rank...@purdue.edu wrote:
Hi all,
I would like to calculate the number of water molecules around any of the
methyl carbon atoms of tert-butyl alcohol. Currently, I have
Dear Justin and all the colleagues,
I am just trying to use g_potential to do the analysis of model. However, one
thing puzzled me is about the slice number -sl.
When different slice numbers are defined, the calculated potential is also
different. I do not know the reason of that. Could you
Hi,
They ought to, and we hope they do, but historically quality control of
analysis tools was threadbare, there is no testing of that kind of thing
now, and certainly no implied warranty. Especially at the existing price
point! ;-)
That comment could easily refer to (or be) an archaic code
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