Hi,
Something went wrong earlier in your workflow. Check your log files, etc.
Mark
On Nov 13, 2013 3:57 AM, guozhicheng222 guozhicheng...@126.com wrote:
Hi:
When I am running the ibi procedure, I get the following error message:
A coordinate in file
Hi:
When I am running the ibi procedure, I get the following error message:
A coordinate in file conf.gro does not
contain a '.'
Additionally, I check the coordinate file of confout.gro in step_001. It showed
that 'nan' symbol appeared in
Hi
I am confusing with the output file (.log) about the sample frequency (frames)
in my simulation. The average information in .log file is 'Statistics over
31 steps using 3001 frames' where nstxout =4000 and nstlog =4000. While,
'Statistics over 31 steps using 20001 frames', appeared
On 11/11/13 5:04 AM, guozhicheng222 wrote:
Hi
I am confusing with the output file (.log) about the sample frequency
(frames) in my simulation. The average information in .log file is
'Statistics over 31 steps using 3001 frames' where nstxout =4000 and
nstlog =4000. While, 'Statistics over
Dear Friends,
I am just a beginner in using GROMCS-4.6.3 and I want to simulate gas
mixture, the same as mixture of O2 and N2, any help(the same as introducing
a reference, not GROMACS manual b/c there is no explanation about gas
mixture) is appreciated.
Kind Regards,
Ali
--
View this message
The principle is the same as at
http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents
On Nov 3, 2013 6:55 PM, ali.nazari ali.nazari.a...@gmail.com wrote:
Dear Friends,
I am just a beginner in using GROMCS-4.6.3 and I want to simulate gas
mixture, the same as mixture of O2 and N2, any
Hello. I was calculating the viscosity of hexane through the Gromacs
command g_energy. Three files are generated: visco.xvg, evisco.xvg and
eviscoi.xvg. The file visco.xvg presents the shear viscosity and bulk, but
the value does not match the experimental. I used 8 ns simulation at
equilibrium.
Hello. I was calculating the viscosity of hexane through the Gromacs
command g_energy. Three files are generated: visco.xvg, evisco.xvg and
eviscoi.xvg. The file visco.xvg presents the shear viscosity and bulk, but
the value does not match the experimental. I used 8 ns simulation at
equilibrium.
If I use the topology and coordinates of a small molecule from ATB for
docking (structure.pdb / structure.itp which match in atom numbering and
sequence); after docking and saving the structure_dock.pdb, the atom
numbering does not match the numbering in the structure.itp file. This
causes
Please don't reply to the entire digest; the archive is hopelessly confused as
it is, but let's not make it any worse ;)
On 9/6/13 2:29 PM, R R S Pissurlenkar wrote:
If I use the topology and coordinates of a small molecule from ATB for docking
(structure.pdb / structure.itp which match in
I am facing a problem while simulating the tRNA molecule
while converting pdb to gro,
Fatal error:
Atom OP3 in residue A 1 was not found in rtp entry RA5 with 31 atoms
while sorting atoms.
force field used 3 (AMBER96 protein, nucleic AMBER94), water model TIP3P.
i checked in gromacs error list,
On 9/4/13 6:04 AM, Prajisha Sujaya wrote:
I am facing a problem while simulating the tRNA molecule
while converting pdb to gro,
Fatal error:
Atom OP3 in residue A 1 was not found in rtp entry RA5 with 31 atoms
while sorting atoms.
force field used 3 (AMBER96 protein, nucleic AMBER94),
Hey :)
Sorry for replying a bit late. But the issues you mention in this and the
other posts are usually solved by closely reading the text of the tutorial,
not only the commands.
Cheers,
Tsjerk
On Sun, Aug 25, 2013 at 3:44 AM, The One And Only chappybo...@gmail.comwrote:
Never mind, I'm
I've moved on from that point; now I'm stuck at where it asks me to remove
molecules of solvent from the topology file.
On Tue, Aug 27, 2013 at 1:33 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hey :)
Sorry for replying a bit late. But the issues you mention in this and the
other posts are
Hi ...,
You should have had a look at the topology file format in an earlier step.
At the end is a listing of molecules. As it says in the tutorial, you
replaced solvent by ions, and you have to make changes in the topology file
to match that replacement. Open the file in an editor, have a look
What kind of editor should I open it in? I have Pymol, but I don't know if
it's the right one.
--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
a text editor
On Tue, Aug 27, 2013 at 1:54 PM, The One And Only chappybo...@gmail.comwrote:
What kind of editor should I open it in? I have Pymol, but I don't know if
it's the right one.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
An editor is a program to edit the text in a file: gedit, nano, vi, emacs,
... It'll be the equivalent of Windows' Notepad. Can you find a tutor
around to help you out with the basic usage of Linux? It's always difficult
to plunge into several different things at the same time, here 'using
linux',
So I started following some tutorials online since I didn't get a response
last time. the tutorial I'm using is:
http://nmr.chem.uu.nl/%7Etsjerk/course/molmod/
I followed that tutorial to the second page and got stuck at the step where
it asks you to input: pdb2gmx -f protein.pdb -o protein.gro -p
It sounds like you dont have the .pdb file in your working directory.
Perhaps you need to learn a bit about unix filesystems
On Sat, Aug 24, 2013 at 6:18 PM, The One And Only chappybo...@gmail.comwrote:
So I started following some tutorials online since I didn't get a response
last time. the
that's something i know nothing about; I just graduated from high school
and I have no background or experience in open source projects or programs
like pymol/gromacs. My professor wants me to be able to produce a setup,
simulation, and analysis within a week so I'm pretty desperate right now in
On 8/24/13 9:26 PM, The One And Only wrote:
that's something i know nothing about; I just graduated from high school
and I have no background or experience in open source projects or programs
like pymol/gromacs. My professor wants me to be able to produce a setup,
simulation, and analysis
so how do i solve the protein.pdb issue?
On Sat, Aug 24, 2013 at 6:37 PM, Justin Lemkul jalem...@vt.edu wrote:
On 8/24/13 9:26 PM, The One And Only wrote:
that's something i know nothing about; I just graduated from high school
and I have no background or experience in open source
Never mind, I'm dumb. I just realized that protein.pdb means i have to
specify which protein i want like 1qlz.pdb and not actually type
protein.pdb BUT THANKS GUYS!!
On Sat, Aug 24, 2013 at 6:40 PM, The One And Only chappybo...@gmail.comwrote:
so how do i solve the protein.pdb issue?
On
Hi everyone,
I am trying to install Gromacs on OS X and following the installation guide, in
section 4.1, I get an output shown as follows:
Sonikas-MacBook-Pro:Downloads sonikagahlawat$ cd gromacs-4.6.2
Sonikas-MacBook-Pro:gromacs-4.6.2 sonikagahlawat$ cmake
cmake version 2.8.11.1
Usage
cmake
Hi Sonika,
cmake needs a specification of the path where the source code is. In
addition to that, it is best to build it in a separate directory. As
explained on the website, in your gromacs directory:
mkdir build
cd build
cmake ../
make
make install
Hope it helps,
Tsjerk
On Tue, Jul 2,
Dear Gmx users,
I need to ask you about a doubt I have regarding changing an analysis tool
in Gromacs. More specifically g_covar. I found the modified source code for
gmx_covar.c [ gmx_covar.c
http://gromacs.5086.x6.nabble.com/file/n5008825/gmx_covar.c ] and I would
like to replace the current
You need to call the newly compiled code. Either install the new version
and source GMXRC appropriately, or use a full path to the new version in
the build tree.
Mark
On Wed, Jun 5, 2013 at 11:05 AM, rohitarora rohitaror...@gmail.com wrote:
Dear Gmx users,
I need to ask you about a doubt I
]
Sent: 01 May 2013 22:58
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] help with g_hydorder and g_polystat
On 5/1/13 8:44 AM, Emmanuel, Alaina wrote:
No, using a trajectory file with g_hydorder hasn't made any difference. The
error is still the same.
When I use g_polystat, I use
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin Lemkul [jalem...@vt.edu]
Sent: 30 April 2013 16:10
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] help with g_hydorder and g_polystat
On 4/30/13 6:24 AM, Emmanuel
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] help with g_hydorder and g_polystat
On 4/30/13 9:00 PM, Emmanuel, Alaina wrote:
Hello Justin,
My mdp file shows that the pbc was set to xyz.
Instead of analyzing a coordinate file, does it work with a trajectory?
Regarding g_polystat
On 5/1/13 8:44 AM, Emmanuel, Alaina wrote:
No, using a trajectory file with g_hydorder hasn't made any difference. The
error is still the same.
When I use g_polystat, I use the following command:
g_polystat_d -f file.xtc -s file.tpr -n polymer_backbone.ndx -p persist.xvg
-o polystat.xvg
Dear All,
I'm fairly new to gromacs and having a bit of problem with the g_hydorder and
g_polystat. Thanks in advanced for your time.
For g_hydorder,
I get a fatal error when I type the following command:
g_hydorder_d -f file.gro -s file.tpr -n waters.ndx -o file1.xpm file2.xpm
Error:
On 4/30/13 6:24 AM, Emmanuel, Alaina wrote:
Dear All,
I'm fairly new to gromacs and having a bit of problem with the g_hydorder and
g_polystat. Thanks in advanced for your time.
For g_hydorder,
I get a fatal error when I type the following command:
g_hydorder_d -f file.gro -s file.tpr -n
for GROMACS users
Subject: Re: [gmx-users] help with g_hydorder and g_polystat
On 4/30/13 6:24 AM, Emmanuel, Alaina wrote:
Dear All,
I'm fairly new to gromacs and having a bit of problem with the g_hydorder and
g_polystat. Thanks in advanced for your time.
For g_hydorder,
I get a fatal error when I
for GROMACS users
Subject: Re: [gmx-users] help with g_hydorder and g_polystat
On 4/30/13 6:24 AM, Emmanuel, Alaina wrote:
Dear All,
I'm fairly new to gromacs and having a bit of problem with the g_hydorder and
g_polystat. Thanks in advanced for your time.
For g_hydorder,
I get a fatal error when I
Hello,
I wanna ask some questions about load imbalance.
1 Here are the messages resulted from grompp -f md.mdp -p topol.top -c npt.gro
-o md.tpr
NOTE 1 [file md.mdp]:
The optimal PME mesh load for parallel simulations is below 0.5
and for highly parallel simulations between 0.25 and
On Wed, Apr 10, 2013 at 10:50 AM, 申昊 shen...@mail.bnu.edu.cn wrote:
Hello,
I wanna ask some questions about load imbalance.
1 Here are the messages resulted from grompp -f md.mdp -p topol.top -c
npt.gro -o md.tpr
NOTE 1 [file md.mdp]:
The optimal PME mesh load for parallel
On Wed, Apr 10, 2013 at 4:50 PM, 申昊 shen...@mail.bnu.edu.cn wrote:
Hello,
I wanna ask some questions about load imbalance.
1 Here are the messages resulted from grompp -f md.mdp -p topol.top -c
npt.gro -o md.tpr
NOTE 1 [file md.mdp]:
The optimal PME mesh load for parallel
(Roberto Benigni, about Roberto Saviano)
Il 21/03/2013 06:37, gmx-users-requ...@gromacs.org ha scritto:
Message: 3 Date: Wed, 20 Mar 2013 13:05:08 -0400 From: Justin Lemkul
jalem...@vt.edu Subject: Re: [gmx-users] help with chromophore of a
GFP To: Discussion list for GROMACS users gmx-users
On Wed, Mar 20, 2013 at 6:01 PM, Anna MARABOTTI amarabo...@unisa.it 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
...@gmail.com [2] Subject: Re: [gmx-users] help with
chromophore of a GFP To: Discussion list for GROMACS users
gmx-users@gromacs.org [3] Message-ID:
camnumasicymgivb_x5sy1yb44th8vknioqvhzdqq-tam9tn...@mail.gmail.com [4]
Content-Type: text/plain; charset=ISO-8859-1 On Wed, Mar 20, 2013 at
6:01 PM
, such that it links to its
neighbours
with normal peptide links.
-- Message: 5
Date: Thu, 21 Mar 2013 11:46:12 +0100 From: Mark Abraham
mark.j.abra...@gmail.com [2] Subject: Re: [gmx-users] help with
chromophore of a GFP To: Discussion list for GROMACS users
gmx-users
Abraham
mark.j.abra...@gmail.com [2] Subject: Re: [gmx-users] help with
chromophore of a GFP To: Discussion list for GROMACS users
gmx-users@gromacs.org [3] Message-ID:
camnumasicymgivb_x5sy1yb44th8vknioqvhzdqq-tam9tn...@mail.gmail.com [4]
Content-Type: text/plain; charset=ISO-8859-1 On Wed, Mar
, such that it links to its
neighbours
with normal peptide links.
-- Message: 5
Date: Thu, 21 Mar 2013 11:46:12 +0100 From: Mark Abraham
mark.j.abra...@gmail.com [2] Subject: Re: [gmx-users] help with
chromophore of a GFP To: Discussion list for GROMACS users
gmx-users
in pdb format
as its easier than jumping back and forth.
Original-Nachricht
Datum: Thu, 21 Mar 2013 21:43:16 +0100
Von: Mark Abraham mark.j.abra...@gmail.com
An: Discussion list for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] help with chromophore of a GFP
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 you know, has a chromophore (CFY) derived from four
residues of the
On Wed, Mar 20, 2013 at 1:01 PM, Anna MARABOTTI amarabo...@unisa.it 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
Hi Steven
I'm running simulations on DNA structures using the amber99sb-ildn FF. I
had no problem generating .top and .gro files
I might be able to help if you are interested.
send me the PDB file.
Yocheved
On Sun, Jan 20, 2013 at 10:57 PM, Tom dna...@gmail.com wrote:
Dear Gromacs User
I
On 1/20/13 3:57 PM, Tom wrote:
Dear Gromacs User
I built DNA with the pdb file and *mol2
But when I used pdb2gmx to obtain *top file, pdb2gmx give error
report when I chose charmm27:
---
Program pdb2gmx, VERSION 4.5.5
Source code file: resall.c, line: 581
Fatal error:
On 1/7/13 6:11 PM, Tom wrote:
Dear Gromacs Users
I want to use harmonic type of improper angle potential with opls-aa
The manu seems not clear.
Can anyone give an small example about the format in *rtp file
and ffbond.itp file?
The names of improper_*_*_*_* tell you to what improper the
Have a look there:
http://virtualchemistry.org/molecules/110-02-1/index.php
virtualchemistry.org is a really nice site (from David van der Spoel,
and others i think), which has many paramters for solvents for the GAFF
and OPLS force field. And also Physical properties for these.
Greetings
On 12/2/12 2:17 AM, 申昊 wrote:
Hi everyone，
I am a new one on using gromacs. Now I have some problems.
[1] I want using g_analyze to calculate the self-ACF with the dist.xvg
resulted from g_dist, the file nameddist.xvg consists two lists of
time(ns) and distance(nm),
Hi everyone，
I am a new one on using gromacs. Now I have some problems.
[1] I want using g_analyze to calculate the self-ACF with the dist.xvg
resulted from g_dist, the file nameddist.xvg consists two lists of
time(ns) and distance(nm), respectively.
(a)why the result shows a
Please unsubscribe. Thank you.
Best,
Marlon
Am 05.10.2012 12:39, schrieb gmx-users-requ...@gromacs.org:
Send gmx-users mailing list submissions to
gmx-users@gromacs.org
To subscribe or unsubscribe via the World Wide Web, visit
On 10/5/12 7:20 AM, Marlon Hinner wrote:
Please unsubscribe. Thank you.
Per the instructions in the footer of every mail on the list:
* Please don't post (un)subscribe requests to the list. Use the www interface or
send it to gmx-users-requ...@gromacs.org.
-Justin
--
Hello Gromacs Users:
I apologize for asking a question that has come up several times in the
forum, but I have read the answers to those posts and I am not still
unable to fix the error based on the suggestions in the previous emails.
It is completely possible that I am just not
On 8/30/12 9:23 PM, Katrina Lexa wrote:
Hello Gromacs Users:
I apologize for asking a question that has come up several times in the
forum, but I have read the answers to those posts and I am not still
unable to fix the error based on the suggestions in the previous emails.
It
Dear All,
I just configured the mdrun-gpu. When I tested mdrun-gpu by running
gromacs-gpubench-dhfr.tar.gz which is from gromacs website. Unfortunately, it
failed with segmentation fault. I don't think the system has any equilibrium
problem since it works fine in mdrun. I will appreciate a
On 28/07/2012 12:58 AM, Du Jiangfeng (BIOCH) wrote:
Dear All,
I just configured the mdrun-gpu. When I tested mdrun-gpu by running
gromacs-gpubench-dhfr.tar.gz which is from gromacs website. Unfortunately, it failed with
segmentation fault. I don't think the system has any equilibrium problem
i am using the tutorial KALP15 in DPPC for my protein in bilipid
membrane SIMULATION.
i have reached Step Three: Defining the Unit Cell Adding Solvent
where i hav to pack the lipids around the protein using InflateGro.
how do i start using inflategro?
my last step was : to generate this new
On 6/15/12 5:58 AM, ankita oindrila wrote:
i am using the tutorial KALP15 in DPPC for my protein in bilipid
membrane SIMULATION.
i have reached Step Three: Defining the Unit Cell Adding Solvent
where i hav to pack the lipids around the protein using InflateGro.
how do i start using
how to do it.
Cheers,
Emmanuel
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Saturday, May 05, 2012 12:59 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Help
Hi
Im trying to calculate the hydration free energy for the molecule Aniline
And I get a free energy value about 10 kcal higher than the experimental value
What I do is I couple vdw then charges from a dummy state and add the two delta
G values using the g_bar method. If you have any idea why is
On 5/4/12 3:56 PM, Milinda Samaraweera wrote:
Hi
Im trying to calculate the hydration free energy for the molecule Aniline
And I get a free energy value about 10 kcal higher than the experimental value
What I do is I couple vdw then charges from a dummy state and add the two delta
G values
Please keep all correspondence on the gmx-users list. I am not a private tutor
and you have better odds of solving your problem by allowing others to provide
input.
On 5/4/12 8:01 PM, Milinda Samaraweera wrote:
Hi Justin
Im a very new to using Gromacs. I tried to reproduce the values in
Hi Guys,
I have done the simulation. The total steps is 500. At around 90 steps,
the error information appear like the followings.
Please give me some suggestions to fix it.
Best wishes,
Desheng
--
Program mdrun, VERSION 4.5.5
On 4/26/12 2:52 PM, Desheng Zheng wrote:
Hi Guys,
I have done the simulation. The total steps is 500. At around 90 steps,
the error information appear like the followings.
Please give me some suggestions to fix it.
Based on the comment that precedes the error call in the code:
On 4/26/12 3:30 PM, Desheng Zheng wrote:
Thanks Justin!
about the Software inconsistency error: Inconsistent DD boundary staggering
limits!
I still have three concerts.
1. Is it ok, if i use grompp to generate the edr file in gromacs 4.5.5
environmentwith the gro file and top file which
and the same commands?
Best wishes,
Desheng
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Thursday, April 26, 2012 3:05 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users
Dear all,
I'm trying to simulate with pbc=xy and I need two walls. My settings are as
follows:
pbc = xy
nwall = 2
wall_atomtype = C C
wall_type = 9-3
wall_r_linpot = -1 -1
wall_density= 20 20
wall_ewald_zfac = 3
The problem
For walls, the atoms in the wall are virtual.
Remember that 9-3 LJ integratees over the volume behind the wall so you will
have to set your atom density appropriately. Setting wall_density to 20/nm^3
for 9-3 wall leads to 20 carbon atoms per nm^3. That's not going to be
totally solid, imo.
I am
*SIMULATION OF LYSOZYME IN WATER USING GROMACS-4.0.5
*
STEP: TO NEUTRALIZE THE +8 CHARGE WITH 8 CL- MOLECULES*
COMMAND GIVEN :
[root@localhost gromacs-4.0.5]# genion -s ions.tpr -o 1AKI_solv_ions.gro -p
topol.top -pname NA -nname CL -nn 8*
:-) G R O M A C S (-:
On 31/03/2012 6:02 PM, oindrila das wrote:
*SIMULATION OF LYSOZYME IN WATER USING GROMACS-4.0.5
*
STEP: TO NEUTRALIZE THE +8 CHARGE WITH 8 CL- MOLECULES*
COMMAND GIVEN :
[root@localhost gromacs-4.0.5]# genion -s ions.tpr -o
1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -nn 8*
Hi Chandran,
What did you try, and what error did it come up with? What platform
are you using, and which version of DSSP? The latest version of DSSP
won't work with Gromacs yet.
Cheers,
Tsjerk
On Mon, Mar 19, 2012 at 2:39 PM, chandran karunakaran
ckaru2...@yahoo.com wrote:
Dear ALL,
On 20/03/2012 12:39 AM, chandran karunakaran wrote:
Dear ALL,
We could not run DSSP for analysing the secondary structure.
Any help in this regard is very much appreciated
***+
Dr.Karunakaran Chandran +
Biophysics Department +
Medical College of Wisconsin
Dear friends
Can someone help me with tutorial on replica exchange dynamics
Thanks in advance
Raghuvir
--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search
On 13/03/2012 3:17 PM, Raghuvir Pissurlenkar wrote:
Dear friends
Can someone help me with tutorial on replica exchange dynamics
Thanks in advance
Raghuvir
Search the GROMACS webpage, please. You will want to do some normal
tutorials to understand normal workflows first.
Mark
--
Hi everybody!
I have a small favor to ask that should hopefully help both us and you in the
long run.
As some of you might know, we have been working quite closely with NVIDIA for a
while to develop a better (and parallel) GPU version of GROMACS to
significantly accelerate simulations. With
Hi everybody,
I am trying to do essential dynamics sampling from a starting structure to
the target structure, so I am using the command:
make_edi_d -f ../eigenvec.trr -eig ../eigenval.xvg -s topol.tpr -radcon 1
-n index.ndx -tar target.gro
The projection of the starting structure and of the
Hi gromacs Users:
I have a doubt respect to how g_hbond consider the cutoff angle (-a)
Acceptor-Donnor-Hydrogen in gromacs 4.5.4. I need to evaluate the hydrogen
bonds with an anble larger than 135°. The default value of the angle is cutoff
in g_hbond is 30°, so this value means that the H.
alejandro esteban blanco munoz wrote:
Hi gromacs Users:
I have a doubt respect to how g_hbond consider the cutoff angle (-a)
Acceptor-Donnor-Hydrogen in gromacs 4.5.4. I need to evaluate the
hydrogen bonds with an anble larger than 135°. The default value of the
angle is cutoff in g_hbond
On 4/01/2012 4:57 PM, Robert Hamers wrote:
I'd appreciate any help --
I'm trying to model a small (~ 20-carbon ) molecule linked to a
diamond surface. I got the diamond surface with 1500 atoms working
fine all the way through to the MD simulation and it looks great. But
I'm getting stuck
Thanks-- that clarifies a lot. I hadn't quite realized how much is
assumed about the residue terminii. It seems like I was trying to fit a
square peg into a round hole. I'm going to re-think this and maybe
take a different approach just based on using HETATMs and not trying to
define a
I'd appreciate any help --
I'm trying to model a small (~ 20-carbon ) molecule linked to a diamond
surface. I got the diamond surface with 1500 atoms working fine all
the way through to the MD simulation and it looks great. But I'm
getting stuck on the molecule, which is not a protein but
Dear all
I run a MD on a GPCR (transmembrane protein)
Then I run a PCA on results and I found 3PC sufficient to explain variance.
On the same PC I get big values for samples located both at Nter
(extracellular) and Cter (intracellular) or for similar cases such as both
Nter(extracellular) and
On 3/01/2012 6:54 AM, Alex Jemulin wrote:
Dear all
I run a MD on a GPCR (transmembrane protein)
Then I run a PCA on results and I found 3PC sufficient to explain
variance.
On the same PC I get big values for samples located both at Nter
(extracellular) and Cter (intracellular) or for similar
Dear All
I run g_density on a membrane protein.
Here are the results
http://elisacarli.altervista.org/densityhead.jpg
http://elisacarli.altervista.org/tailsDensity.jpg
Could you help me to give an interpretation to my analysis?
Thank in advance--
gmx-users mailing list
is a hammer, every problem begins to resemble a nail.
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Alex Jemulin
Sent: Tuesday, 20 December 2011 7:57 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] Help with g_density
Dear All
I run g_density
Hi everyone,
please I have a litle problem:
during my simulation, the dimer I'm simulating changed a lot.
So when I calculate with g_rms, the RMSD between my initial and my final
structure (choosing Protein-H), I get a value of 10 angstroms.
However, when I try to calculate a RMSDeviation
Hi Carla,
during my simulation, the dimer I'm simulating changed a lot.
So when I calculate with g_rms, the RMSD between my initial and my final
structure (choosing Protein-H), I get a value of 10 angstroms.
Have you made sure there are no atoms jumping across the boundaries?
g_rmsf -s
Dear Gromacs Users:
I've been working with small unsaturated hydrocarbons using OPLS-AA with NVT
calculations using box dimensions according to : x=y z=3x centered in
1/2x,1/2y,1/2z in order to obtain surface tension. My system expands at the
begging of the mdrun calculation until it occupies the
I am not sure I can give an affirmative working answer, but you may check
ssh to each node, use top to see whether it's really run or just
occupy the node but not use.
On Sat, Jul 9, 2011 at 8:56 AM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 9/07/2011 3:37 AM, raghu...@bcpindia.org
Hi
I have a problem related to submitting a mdrun job on cluster. I tried
to ask help or gromacs and rocks users-group.
My machine specs.
Cluster of Intel Xeon processors:QC with Rocks Cluster. 8 processors
(16 threads)
When I submit mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px
On 9/07/2011 3:37 AM, raghu...@bcpindia.org wrote:
Hi
I have a problem related to submitting a mdrun job on cluster. I
tried to ask help or gromacs and rocks users-group.
My machine specs.
Cluster of Intel Xeon processors:QC with Rocks Cluster. 8 processors
(16 threads)
When I submit
Hi,
I'm doing implicit solvent in gromacs 4.5.2 with amber03 force field .I have
done energy minimization .Then mdrun in NVT,but there is always LINCS error
.When I make impolicit_solvent=no,it can run successfully. Is there a problem
in the parameter settings? How can I solve the problem?
On 8/07/2011 1:31 PM, wrote:
Hi,
I'm doing implicit solvent in gromacs 4.5.2 with amber03 force field
.I have done energy minimization .Then mdrun in NVT,but there is
always LINCS error .When I make impolicit_solvent=no,it can run
successfully. Is there a problem in the parameter
Dear Mark Abraham all,
We used another benchmarking systems, such as d.dppc on 4 processors,
but we have the same problem (1 proc use about 100%, the others 0%).
After for a while we receive the following error:
Working directory is /localuser/armen/d.dppc
Running on host
This seems to be a problem with your MPI library. Test to see whether other
MPI programs don't have the same problem. If it is not GROMACS specific
please ask on the mailinglist of your MPI library. If it only happens with
GROMACS be more specific about what your setup is (what MPI library, what
Dear Roland,
We need to run the GROMACS on the base of the nodes of our cluster (in
order to use all computational resources of the cluster), that's why we
need MPI (instead of using thread or OpenMP within the SMP node).
I can run simple MPI examples, so I guess the problem on the
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