For people to provide solutions, you will need to show at least what happens
when you use more than six, i.e. the errors you get, structures / topologies
that are not correct etc.
Catch ya,
Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
3
FYI: On your machine running OpenMP across two sockets will probably not be
very efficient. Depending on the input and at how high paralleliation are
you running, you could be better off with running multiple MPI ranks per
GPU. This is a bit of an unexplained feature due to it being complicated to
On 3/21/13 10:35 PM, cqgzc wrote:
Hi
I have been following
http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html(procedure
by Justin) to construct the Polyethylene (PE). However, I can only get the
PE with length 6 just like
CH3-CH2-CH2-CH2-CH2-CH3. Therefore, I want to know how t
Hi
I have been following
http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html(procedure
by Justin) to construct the Polyethylene (PE). However, I can only get the
PE with length 6 just like
CH3-CH2-CH2-CH2-CH2-CH3. Therefore, I want to know how to obtain the long
polymer chain(e.g. l
On 3/21/13 10:20 PM, 라지브간디 wrote:
Dear gmx users,
I am MD simulation for heme ligated protein where i given all bond and angle,
dihedral information in topology file created by pd2gmx ( gromos43a1).
However, i do not know how to interpret the proper and improper dihedrals in
topology file
Dear gmx users,
I am MD simulation for heme ligated protein where i given all bond and angle,
dihedral information in topology file created by pd2gmx ( gromos43a1).
However, i do not know how to interpret the proper and improper dihedrals in
topology file? I have looked over the .rtp file and
On 3/21/13 8:59 PM, Nur Syafiqah Abdul Ghani wrote:
Hi guys,
I have a question..Regarding to my project,i want to make a simulation
between metal and my protein in mix solvent condition.
BUt for gromacs,at the genion part can i run it for two times?
First to make my simulation system is neutr
Hi guys,
I have a question..Regarding to my project,i want to make a simulation
between metal and my protein in mix solvent condition.
BUt for gromacs,at the genion part can i run it for two times?
First to make my simulation system is neutral and the second one is to
use the genion to put the me
Hi Quentin,
That's just a way of saying that something is wrong with either of the
following (in order of possibility of the event):
- your GPU driver is too old, hence incompatible with your CUDA version;
- your GPU driver installation is broken;
- your GPU is behaving in an unexpected/strange ma
I had problems having not used gromacs in years a couple years ago. Try
running it through with the output as a pdb from pdb2gmx, cut off all headers,
and you can then just compare the two files in gedit emacs or word and see
differences. That might help. I routinely just keep everything in p
FYI: As much as Intel likes to say that you can "just run" MPI/MPI+OpenMP
code on MIC, you will probably not be impressed with the performance (it
will be *much* slower than a Xeon CPU).
If you want to know why and what/when are we doing something about it,
please read my earlier comments on MIC p
On 3/21/13 4:43 PM, Mark Abraham wrote:
On Thu, Mar 21, 2013 at 4:30 PM, Anna MARABOTTI wrote:
Dear Mark,
thank you for your message. I'm happy to be on the
right track; unfortunately the end point seems to be very far away...
I tried to obtain that CFY hydrogens and protein hydrogens a
Yes, you can use any kind of FFTW installation for correct results.
Hardware for which FFTW provides no SIMD acceleration will have to fall
back on the generic FFTW routines. (Or you might consider using MKL (or
MKL's FFTW-wrapper feature), which I'd guess Intel supports on MIC. We are
making MKL e
On Thu, Mar 21, 2013 at 4:30 PM, Anna MARABOTTI wrote:
>
>
> Dear Mark,
>
> thank you for your message. I'm happy to be on the
> right track; unfortunately the end point seems to be very far away...
>
>
> I tried to obtain that CFY hydrogens and protein hydrogens are all
> matching the aminoacids
On 3/21/13 3:05 PM, 256B wrote:
Hello Everyone,
I am running MD on a protein with a heme. I want to use gromacs to build a
bond constraint btw a heme and a his. Does anyone know the proper syntax to
do so ?
Consult Chapter 5 of the manual for all topology-related information.
-Justin
--
=
On 3/21/13 2:12 PM, Shima Arasteh wrote:
Dear gmx users,
I have modified the top file of my input.pdb. In this modification I have
deleted 2 atoms, bonds, and diedrals which these deldeted atoms are involved.
The atom numbers of deleted atoms are 2 and 3.
IN grompp I get a fatal error that t
Hello Everyone,
I am running MD on a protein with a heme. I want to use gromacs to build a
bond constraint btw a heme and a his. Does anyone know the proper syntax to
do so ?
- Thank you
--
View this message in context:
http://gromacs.5086.n6.nabble.com/GROMACS-Constraints-tp5006536.html
Se
Dear gmx users,
I have modified the top file of my input.pdb. In this modification I have
deleted 2 atoms, bonds, and diedrals which these deldeted atoms are involved.
The atom numbers of deleted atoms are 2 and 3.
IN grompp I get a fatal error that the top file has not a consecutive numbers
an
On Thu, Mar 21, 2013 at 11:30 AM, Anna MARABOTTI wrote:
>
>
> Dear Mark,
>
> thank you for your message. I'm happy to be on the
> right track; unfortunately the end point seems to be very far away...
>
>
> I tried to obtain that CFY hydrogens and protein hydrogens are all
> matching the aminoacids
Dear Mark,
thank you for your message. I'm happy to be on the
right track; unfortunately the end point seems to be very far away...
I tried to obtain that CFY hydrogens and protein hydrogens are all
matching the aminoacids.rtp entry, in order to avoid dealing with
aminoacids.hdb. This is wha
Hi Carsten,
Actually I tried 4.6.1 weeks ago. Howerev, it seems slighty slower than
old version. It's lucky that I haven't deleted the 4.6.1 build from my
disk. I'm now testing the newest g_tune_pme. It starts up normally but I
have to wait to see the result.
Thanks a lot!
2013/3/21 Carsten
Hi Daniel,
are you using the newest version of 4.6? There was an issue with g_tune_pme,
which I already fixed. I guess it could be responsible for the error that
you see.
Best,
Carsten
On Mar 21, 2013, at 2:26 PM, Daniel Wang wrote:
> Hi everyone~
>
> When I run g_tune_pme_mpi, it prompts
Hi everyone~
When I run g_tune_pme_mpi, it prompts:
Fatal error:
Need an MPI-enabled version of mdrun. This one
(mdrun_mpi)
seems to have been compiled without MPI support.
I'm sure my gromacs is compiled WITH MPI support and "mpiexec -n xx
mdrun_mpi -s yy.tpr" works normally.
How to fix it? I'm
So accordance with Justin's and your statement, SOL_CL_NA coupling would be a
proper option. right?
Thanks for your suggestions
Sincerely,
Shima
From: Gunther Lukat
To: Shima Arasteh ; Discussion list for GROMACS
users
Sent: Thursday, March 21, 2013 4:31 P
I general, I have good results with coupling Ions together with the water.
Dipl.-Inf. Gunther Lukat
g.lu...@gmx.net
www.aplvoro.org
Am 21.03.2013 um 13:56 schrieb Shima Arasteh :
> Hi,
>
> I am simulating a system of POPC/Water/Ions/protein.
> Ions are 1 M NaCL and 3 CL atoms to neutralize
On Thu, Mar 21, 2013 at 8:56 AM, Shima Arasteh
wrote:
> Hi,
>
> I am simulating a system of POPC/Water/Ions/protein.
> Ions are 1 M NaCL and 3 CL atoms to neutralize the system.
>
> In NVT step, I have coupling groups as :
> tc-grps= Protein POPCSOL_CL
>
> comm_grps= Protein_POPC S
Hi,
I am simulating a system of POPC/Water/Ions/protein.
Ions are 1 M NaCL and 3 CL atoms to neutralize the system.
In NVT step, I have coupling groups as :
tc-grps = Protein POPC SOL_CL
comm_grps = Protein_POPC SOL_CL
when I run the grompp for NVT, I get the error that the 615
On 3/21/13 8:10 AM, neeru sharma wrote:
Message: 1
Date: Thu, 21 Mar 2013 07:05:44 -0400
From: Justin Lemkul
Subject: Re: [gmx-users] Restraining water molecule
To: Discussion list for GROMACS users
Message-ID: <514ae988.4050...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=fl
>
> Message: 1
> Date: Thu, 21 Mar 2013 07:05:44 -0400
> From: Justin Lemkul
> Subject: Re: [gmx-users] Restraining water molecule
> To: Discussion list for GROMACS users
> Message-ID: <514ae988.4050...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 3/21/13 4:29
On 3/21/13 7:38 AM, Amit wrote:
Dear Dr. Lemkul,
Many thanks for the reply and suggestion. I
believe doing docking first and then going for simulation is more
relevant as this will lessen the nonspecific interaction. Correct me
if I am wrong. Also I would like to ask o
Dear Dr. Lemkul,
Many thanks for the reply and suggestion. I
believe doing docking first and then going for simulation is more
relevant as this will lessen the nonspecific interaction. Correct me
if I am wrong. Also I would like to ask one more question. I would
like to sim
On 3/21/13 6:30 AM, Shima Arasteh wrote:
Dears,
As I read in some other messages in mailing list, it is supposed to modify
bonds, angles and dihedrals in top file to define a peptide bond for the last
and first residues as well as other peptide bonds.
I am wondering if it is necessary to def
On 3/21/13 5:11 AM, Amit wrote:
Dear Gromacs Users,
I am new to gromacs software and
currently in learning phase. Currently, I am facing a big problem. I have
two proteins namely A and B. Wet lab results have shown that both A and B
interacts with each othe
On 3/21/13 2:12 AM, 라지브간디 wrote:
p{margin:0;padding:0;}
Dear Justin,
I have checked my index.ndx file and it doesnt have any atoms close to 37872
atoms. I am bit confused why its happening.
There is some colossal mismatch between your coordinates, topology, and/or index
file. I wou
On 3/21/13 4:29 AM, neeru sharma wrote:
Message: 6
Date: Wed, 20 Mar 2013 09:04:05 -0400
From: Justin Lemkul
Subject: Re: [gmx-users] Restraining water molecule
To: Discussion list for GROMACS users
Message-ID:
<
caduqwc5+fotchpmi0pqeexcnpkbtqa-yb0px1p889gy3jza...@mail.gmail.com>
Con
On Wed, Mar 20, 2013 at 6:01 PM, Anna MARABOTTI wrote:
>
>
> Dear gmx-users,
>
> it's about two weeks that I'm trying to solve this
> problem, and I can't, so I'm asking your help.
>
> I want to do some MD
> simulations on a protein of the family of green fluorescent protein.
> This protein, as y
Dears,
As I read in some other messages in mailing list, it is supposed to modify
bonds, angles and dihedrals in top file to define a peptide bond for the last
and first residues as well as other peptide bonds.
I am wondering if it is necessary to define pairs too?
Thanks in advance.
Sincer
That's probably a free-energy plot, made by some tool that works like
g_sham. Every structure can be projected onto the coordinates of the
underlying 2D histogram.
Mark
On Thu, Mar 21, 2013 at 10:42 AM, Albert wrote:
> Hello:
>
> I've finished a replica exchange simulation and I would like to
Hello:
I've finished a replica exchange simulation and I would like to make
a plot like:
http://ars.els-cdn.com/content/image/1-s2.0-S1093326303002006-gr4.jpg
I am just wondering how can associate your energy (the red/white color)
with 2D XY plot in the above figure?
thank you very much
Dear Gromacs Users,
I am new to gromacs software and
currently in learning phase. Currently, I am facing a big problem. I have
two proteins namely A and B. Wet lab results have shown that both A and B
interacts with each other by co-immunoprecipitation technique
Dear Justin,
there is not a "unique" GFP chromophore, the chromophore I am dealing
with is not the same for which CHARMM parameters have been published (I
am aware of CHARMM parameters for p-hydroxybenzylideneimidazolinone
chromophore of green fluorescent protein published by Reuter et al 2002,
> Message: 6
> Date: Wed, 20 Mar 2013 09:04:05 -0400
> From: Justin Lemkul
> Subject: Re: [gmx-users] Restraining water molecule
> To: Discussion list for GROMACS users
> Message-ID:
> <
> caduqwc5+fotchpmi0pqeexcnpkbtqa-yb0px1p889gy3jza...@mail.gmail.com>
> Content-Type: text/plain; char
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