Hi,
Something went wrong earlier in your workflow. Check your log files, etc.
Mark
On Nov 13, 2013 3:57 AM, "guozhicheng222" wrote:
> Hi:
>
> When I am running the ibi procedure, I get the following error message:
>
>
>
> A coordinate in file conf.gro does
>
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
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" 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 help(the same as intro
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 at
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), water
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',
a text editor
On Tue, Aug 27, 2013 at 1:54 PM, The One And Only wrote:
> 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
> * Please search
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
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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 ar
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 wrote:
> Hey :)
>
> Sorry for replying a bit late. But the issues you mention in this and the
> other posts are usually solve
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 wrote:
> Never mind, I'm dumb. I just realized t
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 wrote:
> so how do i solve the protein.pdb issue?
>
>
> On Sat, Aug 24, 2013
so how do i solve the protein.pdb issue?
On Sat, Aug 24, 2013 at 6:37 PM, Justin Lemkul 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 projects or pro
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 withi
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
te
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 wrote:
> So I started following some tutorials online since I didn't get a response
> last time. the tutorial I'm using i
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, 2013
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 wrote:
> Dear Gmx users,
>
> I need to ask you about a doubt I have regarding chang
t.edu]
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.
>
&
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
y 2013 10:58
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 traje
laina
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, Emm
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
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
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
On Wed, Apr 10, 2013 at 4:50 PM, 申昊 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 simulations is below 0.5
On Wed, Apr 10, 2013 at 10:50 AM, 申昊 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 simulations is below 0.5
pdb format
as its easier than jumping back and forth.
Original-Nachricht
> Datum: Thu, 21 Mar 2013 21:43:16 +0100
> Von: Mark Abraham
> An: Discussion list for GROMACS users
> Betreff: Re: [gmx-users] help with chromophore of a GFP
> On Thu, Mar 21, 2013 a
estion was to create a new
entry in the .rtp file of the selected forcefield.
Indeed, this
kind of problem is most easily solved by making a new
"residue" that
contains the whole chromophore, such that it links to its
neighbours
with normal peptide links.
involving residue CFY.
>
Yeah, but my bet is those atoms are the C-terminus and N-terminus of the
fragments that should form peptide bonds to CFY.
Mark
> Any help is
> welcome
>
> Thank you so much.
>
> Anna
>
> Il 21.03.2013 12:00
> gmx-users-requ...@gromacs.org ha scr
ch.
>
> Anna
>
> Il 21.03.2013 12:00
> gmx-users-requ...@gromacs.org ha scritto:
>
> >> 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 p
to its
> neighbours
with normal peptide links.
> -- Message: 5
Date: Thu, 21 Mar 2013 11:46:12 +0100 From: Mark Abraham
Subject: Re: [gmx-users] help with
chromophore of a GFP To: Discussion list for GROMACS users
Message-ID:
Content-Type: text/plain; charset=IS
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
an with a pen, the man with the gun is a dead
man"
(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
Subject: Re: [gmx-users] help with chromophore of a
GFP
On Wed, Mar 20, 2013 at 1:01 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
On 2/26/13 7:46 AM, Sjøli Stian wrote:
dear gmx-users,
this is a stupid question (and partially a test of use). I cant find any
information on how to use/modify maxvarn as a parameter for grompp. Can you
point to examples or literature?
Consider the help text:
-maxwarn int0
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 wrote:
> Dear Gromacs User
>
> I built DNA with t
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:
R
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 p
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), respectively
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
--
===
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
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 proble
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 infl
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
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 sh
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 usi
file
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
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 whic
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:
/*
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
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*
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 +
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
wrote:
> Dear ALL,
>
> We could not r
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
--
gmx-us
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 i
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 sepa
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
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 ca
What is your interpretation?
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is
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
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 wrote:
> On 9/07/2011 3:37 AM, raghu...@bcpindia.org wrote:
>>
>> Hi
>>
>>
>> I
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 md
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 settings
On 4/28/2011 4:44 AM, Hrachya Astsatryan wrote:
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 exa
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
implementat
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
ha
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 wn1.ysu-cluster.gr
On 4/22/2011 5:40 PM, Hrachya Astsatryan wrote:
Dear all,
I would like to inform you that I have installed the gromacs4.0.7
package on the cluster (nodes of the cluster are 8 core Intel, OS:
RHEL4 Scientific Linux) with the following steps:
yum install fftw3 fftw3-devel
./configure --prefix=
On 7/04/2011 9:38 PM, Peter C. Lai wrote:
Ok here's a minor? problem I'm having with dihedrals.
Apparently grompp won't read H-H dihedrals such as:
HGA2 CG321 CG321 HGA2 9 0.000.92048 3 ;LIPID alkane
HGA2 CG321 CG331 HGA3 9 0.000.66944 3 ;PROT rot
Ok here's a minor? problem I'm having with dihedrals.
Apparently grompp won't read H-H dihedrals such as:
HGA2 CG321 CG321 HGA2 9 0.000.92048 3 ;LIPID alkane
HGA2 CG321 CG331 HGA3 9 0.000.66944 3 ;PROT rotation
barrier in ethane
(the lipid equiv wo
On 7/04/2011 5:39 PM, Peter C. Lai wrote:
Actually I figured it out.
in forcefield.itp,
the nonbonded.itp file must be included before the bonded.itp file...
Yep, it has the [atomtypes].
Mark
On 2011-04-07 02:22:38AM -0500, Mark Abraham wrote:
On 7/04/2011 3:45 PM, Peter C. Lai wrote:
Ok
Actually I figured it out.
in forcefield.itp,
the nonbonded.itp file must be included before the bonded.itp file...
On 2011-04-07 02:22:38AM -0500, Mark Abraham wrote:
> On 7/04/2011 3:45 PM, Peter C. Lai wrote:
> > Ok I'm now getting the dreaded "Unknown bond_atomtype CG2O5"
> > grompp fatal er
On 2011-04-07 02:01:47AM -0500, Mark Abraham wrote:
> On 7/04/2011 3:45 PM, Peter C. Lai wrote:
> > Ok I'm now getting the dreaded "Unknown bond_atomtype CG2O5"
>
> On what line of what file? Please copy and paste the whole error
> message. Keeping information back only hurts you :-)
Here is the
On 7/04/2011 3:45 PM, Peter C. Lai wrote:
Ok I'm now getting the dreaded "Unknown bond_atomtype CG2O5"
grompp fatal error. I ran pdb2gmx on a pdb of my ligand and it generated
a gro and a top file:
http://pastebin.com/HL3k7EPU for the gro
http://pastebin.com/y6T4ir7y for the top
I ran "grompp -
On 7/04/2011 3:45 PM, Peter C. Lai wrote:
Ok I'm now getting the dreaded "Unknown bond_atomtype CG2O5"
On what line of what file? Please copy and paste the whole error
message. Keeping information back only hurts you :-)
Mark
grompp fatal error. I ran pdb2gmx on a pdb of my ligand and it g
Ok I'm now getting the dreaded "Unknown bond_atomtype CG2O5"
grompp fatal error. I ran pdb2gmx on a pdb of my ligand and it generated
a gro and a top file:
http://pastebin.com/HL3k7EPU for the gro
http://pastebin.com/y6T4ir7y for the top
I ran "grompp -f em.mdp -c nonanone.gro -p nonanone.top -o
Warren Gallin wrote:
On 2011-04-06, at 10:58 AM, Justin A. Lemkul wrote:
Warren Gallin wrote:
I am trying to use g_bar to derive a PMF curve from non-equilibrium
trajectory data. I am using v 4.5.4 on a Mac running OSX 10.6.7.
I am using the end-to-end distance of a peptide as the co-ordin
On 2011-04-06, at 10:58 AM, Justin A. Lemkul wrote:
>
>
> Warren Gallin wrote:
>> I am trying to use g_bar to derive a PMF curve from non-equilibrium
>> trajectory data. I am using v 4.5.4 on a Mac running OSX 10.6.7.
>> I am using the end-to-end distance of a peptide as the co-ordinate of
>>
Warren Gallin wrote:
I am trying to use g_bar to derive a PMF curve from non-equilibrium
trajectory data. I am using v 4.5.4 on a Mac running OSX 10.6.7.
I am using the end-to-end distance of a peptide as the co-ordinate of
interest. After doing a long simulation of the peptide, I selected t
On 2011-04-06 01:49:50AM -0500, Mark Abraham wrote:
> The standard CHARMM .prm files give an indication of how the parameters
> will be used, so it's just a matter of converting units and taking care
> of any constants.
Looks like if I use
http://lists.gromacs.org/pipermail/gmx-users/2010-Septem
Yes, Mark is exactly correct about the glitch. I had just forgotten to
change this default charge in the ffnonbonded.itp when copying from
another atom. As mentioned this has no impact as these charges are never
used by pdb2gmx.
Cheers
Tom
Mark Abraham wrote:
On 6/04/2011 2:51 PM, Peter C.
On 6/04/2011 2:51 PM, Peter C. Lai wrote:
Hello
I am constructing a ligand for which I wish to use the new Charmm CGenFF
parameters (a long aliphatic ketone).
I am using Tom/Par's charmm36 lipid conversion as a baseline template for
comparison:
For reference, c36 lipid CTL3 atoms (in the case
Raghuvir R S Pissurlenkar wrote:
Dear Justin
I removed the constrain on the DPPC molecules, however I find still
LINCS errors are prominent
Any alterative can I try
Reduce the pull_rate. If you pull too fast, your system cannot adapt properly
to the collisions that are induced by the ar
raghu...@bcpindia.org wrote:
Dear Users and Developers
I am trying to execute md_pull.mdp {given below} on a small molecule
embedded at the core of lipid bilayer. I have tried to modify the
md_pull.mdp from the Tutorial by Justin Lemkul on Umbrella sampling. I
encounter LINCS warning (10
kala wrote:
Dear friends
I am trying to run a MD simulation with a Zn ion in the
active site. The zinc makes covalent bond to His , Asp , Cys and Drug
molecule. however I am trying to study various ligands that make a
sustainable bond with zn over period of time. I am new to
Best place to start is to provide an exact copy paste of the command you
used, then an exact copy/paste of the error message.
A good resource for errors is
http://www.gromacs.org/Documentation/Errors and searching the emailing
list http://www.gromacs.org/Support/Mailing_Lists/Search
Catch
Dear Justin,
You're right, I corrected the box vectors , and it works!
Thanks,
--
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/Search before posting!
Please don't pos
Aldo Segura wrote:
Thanks for your answer. You're right in the procedure for the packing
of the protein and lipids. However, after several iterations (~30) the
lipids are packaged to form the bilayer and the protein is outside of
it. I can send you a couple of pictures for a better explanation
Thanks for your answer. You're right in the procedure for the packing
of the protein and lipids. However, after several iterations (~30) the
lipids are packaged to form the bilayer and the protein is outside of
it. I can send you a couple of pictures for a better explanation of my
problem.
Best
Aldo Segura wrote:
Dear gmxusers,
I need to perform molecular dynamics simulation of a B2AR within the
POPC membrane. I have downloaded the 128b.pdb, popc.itp and lipid.itp
files from Prof.Tieleman's group. My protein of interest is 343
residues. Also, I aligned the protein and membrane. I fol
Tanos Franca wrote:
Dear users,
We are trying to perform a MD simulation of a protein with a heme group
using the
gromos53a6 force field but, when trying to run grompp, we receive the
error mesage:
Program grompp, VERSION 4.0.3
Source code file: ../../../../src/kernel/toppush.c, line: 947
F
onetwo wrote:
Hello All,
I want to know one thing that if MD could be used in my case, i have a
protein for which crystal structure is known with a conenzyme bound to
it. It is given in literature that related proteins of this family shows
large conformational change near the substrate bind
Subhrangshu Supakar wrote:
Hi!!
I am new to short peptide simulations at low temperatures.
I want to run a MD of short peptides of 6 - 12 residues at 276 K.
For this the scheme I wish to follow is :
1. Run a short energy minimization of the peptide + water system to
remove short contacts
2.
On 14/10/2010 7:19 PM, Sathish wrote:
Dear all,
I have installed gromacs 4.5.1 in RHEL5.5 server. Then i was started
to run demo but still its running ( more then 5 hrs). How long will
take time to complete.
Any other possible way is there to increase speed ?
Anybody can help me?
It's proba
tekle...@ualberta.ca wrote:
Dear Justine,
As for the distance, have you corrected for PBC? Are you analyzing the
molecules that you think you are?
No, I did not correct for the PBC. How can I do that. And what is the
purpose of that in the g_dist calculation.
Usually one uses trjconv. I
Dear Justine,
As for the distance, have you corrected for PBC? Are you analyzing
the molecules that you think you are?
No, I did not correct for the PBC. How can I do that. And what is the
purpose of that in the g_dist calculation.
Yes,
I just look at the last frame of my simulation and
tekle...@ualberta.ca wrote:
Dear Gmx users,
After working for quite sometime I managed to simulated almost all my
molecules for 20ns. Thank you for all your help especially Justine.Now I
am on last stage of analyzing my data.
First:
I want to calculate g(r)and I used the following command
Dear Gmx users,
After working for quite sometime I managed to simulated almost all my
molecules for 20ns. Thank you for all your help especially Justine.Now
I am on last stage of analyzing my data.
First:
I want to calculate g(r)and I used the following command
g_rdf -f PAP_20ns.xtc -s PA
- Original Message -
From: Alan
Date: Wednesday, August 25, 2010 0:10
Subject: Re: [gmx-users] help with git
To: Discussion list for GROMACS users
> Sorry if confused... because I am *really* confused too with git.
> Anyway, I started anew again and it seems to be working now.&
1 - 100 of 233 matches
Mail list logo
