hello:
I wondering are the three thermostat methods: Langevin, Berendsen and
Nose-Hoover chain are all compatible with semi-isotropy coupling style?
If I would like to use semi-isotropy coupling method, which one would be
better?
thank you very much
best
Albert
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gmx-users mailing list
Thanks a lot Peter.
Will try out with this.
-Anirban
On Wed, May 2, 2012 at 9:42 PM, Peter C. Lai wrote:
> http://uab.hyperfine.info/~pcl/files/popc36/
>
> These were generated for the following work: (please reference):
> Lai, P.C. and Crasto, C.J.
> Beyond Modeling: All-Atom Olfactory Recepto
using? For versions >= 3.0, the above
>> syntax is not allowed anymore, afair.
>>
>> Best
>>
>> Martin
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Plea
On 03/05/12, mu xiaojia wrote:
> Dear gmx users,
>
> I have a question about using the trjconv -pbc options before analyzing my
> trajectory. It's stated by Justin's tutorial that:
>
>
>
> "use trjconv to account for any periodicity in the system. The protein will
> diffuse through th
On 5/2/12 8:55 PM, mu xiaojia wrote:
Dear gmx users,
I have a question about using the trjconv -pbc options before analyzing my
trajectory. It's stated by Justin's tutorial that:
"use trjconv to account for any periodicity in the system. The protein will
diffuse through the unit cell, and may
Dear gmx users,
I have a question about using the trjconv -pbc options before analyzing my
trajectory. It's stated by Justin's tutorial that:
"use trjconv to account for any periodicity in the system. The protein will
diffuse through the unit cell, and may appear to "jump" across to the other
sid
The problem is that functype 1 for [ pairtypes ] when gromacs uses a CHARMM
forcefield is that gromacs treats them as 1-4 interactions. You will have to
ask/wait for someone familiar with the gromacs source to say if there is a
different functype available to use to override non-1-4 interactions
pull_k1 is missing in your input, so it is probably set to 0.
I do not know whether it is used in constraint mode, though.
--
View this message in context:
http://gromacs.5086.n6.nabble.com/Pull-code-for-Constraint-tp4946900p4947436.html
Sent from the GROMACS Users Forum mailing list archive at
Dear Mr. Peter C. Lai,
I appreciate your kind response.
I apologize for the delay on my part.
This NBFIX parameters that I'm working with came from the str file in
http://terpconnect.umd.edu/~jbklauda/research/download/chol_new.str , which
dates from 2012.
I successfully converted this whole fi
I am trying to pull a subdomain of protein towards the center of the channel
it makes. To do this I need to pull some aminoacids in -1, 0, 0 direction. I
tried with this pull code
; Pull code
pull= umbrella
pull_geometry = direction_periodic
pull_start = yes
pull_nstfout= 1
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Krzysztof Kuczera [kkucz...@ku.edu]
Sent: Wednesday, May 02, 2012 6:38 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] pullf.xvg
Could someone please tell me
On 5/2/12 1:09 PM, Sangita Kachhap wrote:
I have to do MD simulation of ligand bound membrane protein in lipid bilayer.
Thus I am doing tutorialfor Protein - Ligand tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
I have used following comma
Hi,
I try to pull the small molecule from the bulk solution to the surface by the
Constraint function.
However, it seems that it does not work well.
Here my part of run parameters about the Constraint in my mdp file
##
constraints = all-bonds; hbonds; all-bonds
Could someone please tell me what exactly is printed in the pullf.xvg
file from an umbrella sampling simulation?
Is it the total force acting the COM of the pull group - i.e. force from
regular potential plus the umbrella force or just the unbiased force?
Krzysztof Kuczera
--
Krzysztof Kuczer
I have Python 2.6.5
2012/5/2 Martin Hoefling
> Am 30.04.2012 19:32, schrieb Thales Kronenberger:
>
> Hey Folks,
>
> > SUDO_USER=laboratorio24
> > PWD=/home/laboratorio24/OpenMM4.0-Linux64/python
> > File "setup.py", line 165
> > print "%s" % outputString
> > ^
> > SyntaxError:
Am 30.04.2012 19:32, schrieb Thales Kronenberger:
Hey Folks,
> SUDO_USER=laboratorio24
> PWD=/home/laboratorio24/OpenMM4.0-Linux64/python
> File "setup.py", line 165
> print "%s" % outputString
> ^
> SyntaxError: invalid syntax
> INSTALLATION FAILED
which python version are yo
here, Gromacs ignore it because *each
>> cystein is on a different chain*. So it adds H and therefor the
>> disulfide bond is ruined during energy minimization.
>> Is there any way to recreate such a disulfide bond (Please don't tell
>> me again about "-ss&q
On 2012-05-02 06:13:04PM +0200, Mirco Wahab wrote:
> Hello Peter,
>
> Am 02.05.2012 17:44, schrieb Peter C. Lai:
>
> > You can wait for ivy bridge, then stick some Kepler GPUs (nvidia gtx
> > 680) in it. That should max the performance. asm is pretty much stagnant
> > for general purpose procs si
Hello Peter,
Am 02.05.2012 17:44, schrieb Peter C. Lai:
You can wait for ivy bridge, then stick some Kepler GPUs (nvidia gtx
680) in it. That should max the performance. asm is pretty much stagnant
for general purpose procs since core2 came out.
Is this true?
To my knowledge, the Fermi GPU (
http://uab.hyperfine.info/~pcl/files/popc36/
These were generated for the following work: (please reference):
Lai, P.C. and Crasto, C.J.
Beyond Modeling: All-Atom Olfactory Receptor Model Simulations
Front. Gene.
Volume 3 Year 2012 Number 61
DOI: 10.3389/fgene.2012.00061
On 2012-05-02 05:49
When considering compute hardware today, you're gonna have to shop like a
gamer. A rig that can get high Battlefield 3 or Arma 2/3 framerates should also
be able to get you some nice ns/day.
I think most people consider Bulldozer mostly a flop. AMD masks lower cycle
speeds with more cores per c
salam,
man mishnasametun?
mozoe naghashie chiye?
2012/5/2 Shima Arasteh
>
> سلام
> یه خواهش دارم. من بعد قاب کردن نقاشی، ازش عکس نگرفتم. لطفا اگر تونستین
> برام چندتا عکس خوب بگیرین
> مرسی
> میشه لطفا؟
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailm
Thanks for your kind reply .
Sincerely,
Shima
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Wednesday, May 2, 2012 7:02 PM
Subject: Re: [gmx-users] GROMOS87 and CHARMM27
On 5/2/12 10:30 AM, Shima Arasteh wrote:
>
> Thanks for your rep
Dear gmx users,
I am so sorry to send a wrong email.
My last mail sent to mailing list sent by mistake.
Sorry
Shima
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Sear
On 5/2/12 10:30 AM, Shima Arasteh wrote:
Thanks for your reply.
What do you mean by running for some additional time?
You're introducing a new force field, which includes different representation of
atoms and a different potential energy function. You can't just take a
configuration gene
سلام
یه خواهش دارم. من بعد قاب کردن نقاشی، ازش عکس نگرفتم. لطفا اگر تونستین برام
چندتا عکس خوب بگیرین
مرسی
میشه لطفا؟--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/
On 2/05/2012 7:49 PM, Lara Bunte wrote:
Hi
I need a little help in using Linux. I wrote this script for the bash, that I
called g_select_script.sh:
#!/bin/bash
g_select -s mol_in_water.pdb -select '"Close to ISO" resname SOL and within 0.4
of resname ISO' -on
make_ndx -f mol_in_water.pdb -o
On 5/2/12 8:14 AM, Sangita Kachhap wrote:
Hello all
I have to do MD simulation of ligand bound membrane protein in lipid bilayer.
Thus I am doing tutorialfor Protein - Ligand tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
I have used foll
On 2/05/2012 8:55 PM, Hagit G wrote:
Hi gmx users,
Well, I saw this question but the answer was not understood.
I'm trying to work with the file 1PPB.pdb. There are 2 chains
connected with a disulfide bond. Gromacs automatically adds H atoms.
Although the disulfide bond is there, Gromacs ignore
On 5/2/12 6:55 AM, Hagit G wrote:
Hi gmx users,
Well, I saw this question but the answer was not understood.
I'm trying to work with the file 1PPB.pdb. There are 2 chains connected with a
disulfide bond. Gromacs automatically adds H atoms.
Although the disulfide bond is there, Gromacs ignore
On 5/2/12 6:49 AM, Anni Kauko wrote:
>
>
> Anni Kauko wrote:
> > Hi!
> >
> > I try to perform pmf calculations for case where a peptide
>>> shifts
> > through the membrane. My COM differences should vary from
On 5/2/12 12:21 AM, Shima Arasteh wrote:
Dear Justin,
I don't want to compare the forcefields results.
Yes, Iwant to use some old information in conjunction with something new.
In fact, I have to regenerate a structure, which has modulated using gmx.ff.
After it, I am going to study it using u
Hi all, I want to be sure to understand what I'm doing with tabulated
potentials.
I'm using tabulated bonds, angles, dihedrals and non-bnding potentials.
1) If I don't specify 1-4 interactions (nrexcl = 3 and gen-pairs =
no), they're all zero for the 1-4 atoms involved in tabulated
dihedrals?
Tha
Hi ALL,
I was looking for a CHARMM36 format (atom-types) equilibrated POPC bilayer
(PDB/GRO) to use with the CHARMM36 FF in GROAMCS 4.5.5. I downloaded one
from Dr. Klauda's site (
http://terpconnect.umd.edu/~jbklauda/research/download.html), but that
popc.pdb (under CHARMM36 FF) seem to have diff
Hello all
I have to do MD simulation of ligand bound membrane protein in lipid bilayer.
Thus I am doing tutorialfor Protein - Ligand tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
I have used following command:
pdb2gmx -f 3HTB_clean.pdb -o c
Hi gmx users,
Well, I saw this question but the answer was not understood.
I'm trying to work with the file 1PPB.pdb. There are 2 chains connected
with a disulfide bond. Gromacs automatically adds H atoms.
Although the disulfide bond is there, Gromacs ignore it because *each
cystein is on a diffe
> >
> >
> > Anni Kauko wrote:
> > > Hi!
> > >
> > > I try to perform pmf calculations for case where a peptide
> >>> shifts
> > > through the membrane. My COM differences should vary from
> > 2.3 to
> > -2.5.
> > >
>
For CPU performance comparison look at:
www.spec.org/cpu2006/results
for each CPU look at the statistics for floating point operations, namely
for SPECfp_base2006 score for the programs of interest (GAMESS, GROMACS,
NAMD, etc.).
For graphics cards you can look at the same site for GPU availabili
On Tue, May 1, 2012 at 9:55 PM, Justin A. Lemkul wrote:
> On 5/1/12 2:40 PM, Lara Bunte wrote:
>> g_select -s molecule.pdb -select '"Close to ISO" resname SOL and within
>> 1.2 of resname ISO'
>>
>> and
>>
>> trjconv -n index.ndx -f molecule.pdb -s molecule.pdb -o output.pdb
>>
>> I got only water
Hi people,
we plan to buy some computer mostly for gromacs, so I want to ask you
for some hints. I'd tried to do some research, but no success. :(
Have someone ever compared AMD Bulldozer and Sandy/Ivy Bridge
architectures? Are there planed any optimizations in gmx core in asm
parts? (if ther
Hi
I need a little help in using Linux. I wrote this script for the bash, that I
called g_select_script.sh:
#!/bin/bash
g_select -s mol_in_water.pdb -select '"Close to ISO" resname SOL and within 0.4
of resname ISO' -on
make_ndx -f mol_in_water.pdb -o index2.ndx
cat index2.ndx index.ndx > ind
On 2/05/2012 5:37 PM, Mark Abraham wrote:
On 2/05/2012 5:12 PM, Anik Sen wrote:
Hi,
Am Anik Sen, using gromacs 3.3.2 version. I have a very simple
question to ask,
In the mdp file, like the emmod.mdp or run.mdp needed for a MD run
there are three factors namely,rlist, rcoulomb and rvdw
On 2/05/2012 5:12 PM, Anik Sen wrote:
Hi,
Am Anik Sen, using gromacs 3.3.2 version. I have a very simple
question to ask,
In the mdp file, like the emmod.mdp or run.mdp needed for a MD run
there are three factors namely,rlist, rcoulomb and rvdw.
1. Is there any minimum value for these t
Hi,
Am Anik Sen, using gromacs 3.3.2 version. I have a very simple question
to ask,
In the mdp file, like the emmod.mdp or run.mdp needed for a MD run there are
three factors namely, rlist, rcoulomb and rvdw.
1. Is there any minimum value for these three below which the results will be
ab
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