On 25/04/2012 3:24 PM, Albert wrote:
hello:
it is blue gene P. And the gromacs is single precision in the
cluster. Getting Loaded...And the administrator told me that I have to
use the multiples of 32 in the bg_size parameter. The number specified
in -np should be 4 times bg_size.
Yes,
Please do not make unsolicited general GROMACS inquiries to private
email addresses. The mailing lists exist for these kinds of purposes.
On point, you cannot be helped unless you provide the command lines that
you used and describe the objectives you were trying to achieve.
Whatever changes
On 25/04/2012 6:28 AM, PAVAN PAYGHAN wrote:
Dear Gromacs Users,
I am using gromacs version is 4.5.3.and running my jobs on single node
with 8 cores.
I have two different systems which contain about 425000 atoms (protein
+ Lipid +SOL) one with bound ligand
and another one unbound
On 26/04/2012 10:47 PM, PAVAN PAYGHAN wrote:
Dear Mark,
Thanks a lot for the reply and highlighting the cause of error that I
was facing.
Still can it be possible to overcome the same error with the available
facility.
Unfortunately you're forcing me to guess the context for this
On 27/04/2012 3:53 PM, seera suryanarayana wrote:
Respected sir,
While i am running the gromacs software i am
getting the following error.Kindly tell me how to over come the error.
Fatal error:
Atom HA in residue LYS 1 was not found in rtp entry LYSH with 15 atoms
while
On 27/04/2012 5:07 PM, seera suryanarayana wrote:
Respected Sir,
While i am running the gromacs software i am
getting the following error.Kindly knowing how to over come the error.
Fatal error:
Residue 'CCN' not found in residue topology database
On 27/04/2012 11:07 PM, Marcelo Lopez wrote:
Hi all,
I'm trying to run a coarse grained system with tabulated non-bonding
potentials for 3 kind of particles. I need to set all the 1-4
interactions to zero
Why not use nrexcl = 3 in your [moleculetype] like the example in manual
5.7.1? (and
On 27/04/2012 10:59 PM, Tomek Wlodarski wrote:
Hi,
I have notice that quite often people in REMD simulation use replicas
in lower than 300K temp.
Using for example temperature ranges from 250 to 450K
I am wondering what is the purpose of those replicas.
I have limited computational resources
On 27/04/2012 5:21 AM, Ricardo O. S. Soares wrote:
Dear users,
In GROMACS, does CHARMM36 ff, calculate eventual 1-4 interactions that
are absent from the [pairtypes] section of the ffnonbonded.itp file?
I ask this because I'm converting cholesterol parameters from
CHARMM36c to gmx format, and
to the foregoing.
Mark
Thanks.
Marcelo Lopez
El día 27 de abril de 2012 10:38, Mark Abraham
mark.abra...@anu.edu.au escribió:
On 27/04/2012 11:07 PM, Marcelo Lopez wrote:
Hi all,
I'm trying to run a coarse grained system with tabulated non-bonding
potentials for 3 kind of particles. I need to set
On 28/04/2012 3:33 AM, Ho, Tuan A. wrote:
Dear Gromacs users,
I would like to simulate a thin film of SWM4_DP water on graphite
surface. First, I equilibrate the water only (run very well), then I
add a graphite surface on it. I freeze the graphite surface but the
graphite surface acted
much.
Any idea for this problem is highly appreciated since I am not sure if
I will be able to perform a parallel job.
Tuan.
*From:*gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Mark Abraham
*Sent:* Friday, April 27, 2012 6:36 PM
*To:* Discussion list
On 28/04/2012 2:04 PM, Albert wrote:
hello:
I am running NPT on a blue gene cluster, but the jobs always failed
with following messages. However, everything goes well if I run it on
my local cluster:
Systems with marginally stable initial conditions can do this. See
. If you prepare the system slightly
better and/or equilibrate more gently, then it will run under BlueGene,
from your evidence of what I assume to be lucky good behaviour on your
workstation.
Mark
THX
ALbert
On 04/28/2012 07:36 AM, Mark Abraham wrote:
On 28/04/2012 2:04 PM, Albert wrote
On 29/04/2012 7:02 PM, Hagit G wrote:
I'm trying to work on thrombin pdf file with 2 chains. The pdb code is 1PPB.pdb
The main problem is: When I use pdb2gmx it adds H atoms to Cys,
hence the disulfide bonds are no longer conected after energy minimization.
How can I avoid this addition of H
On 29/04/2012 7:32 PM, Shima Arasteh wrote:
Actually, I am confused somehow.
I want to equilibrate the system. It contains popc and water. To
equilibrate it, using .mdp file I use the nvt.mdp file as below.
title= NVT equilibration for POPC
define= -DPOSRES; position
On 30/04/2012 3:38 PM, Anirban Ghosh wrote:
On Sat, Apr 28, 2012 at 10:22 PM, Andrew DeYoung
adeyo...@andrew.cmu.edu mailto:adeyo...@andrew.cmu.edu wrote:
Hi,
Typically, I use Gromacs 4.5.5 compiled with automatic threading.
As you
know, automatic threading is awesome
On 30/04/2012 6:34 PM, Steven Neumann wrote:
On Fri, Apr 27, 2012 at 5:13 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
On 4/27/12 12:09 PM, Steven Neumann wrote:
On Fri, Apr 27, 2012 at 4:38 PM, Justin A. Lemkul
jalem...@vt.edu
On 30/04/2012 7:49 PM, seera suryanarayana wrote:
Dear all gromacs users,
I tried the grompp and i got the following error.number of
coordinates in coordinate file (4INS_b4ion.gro, 90396)
does not match topology (4INS.top,
90393).
On 1/05/2012 12:02 PM, cuong nguyen wrote:
Dear Gromacs Users,
I used the command genbox -cs spc216.gro -o box1.g96 -p topol.top
-box 3 3 10 to create box of 3010 water molecules. However, now I
need to create a same size box with only 846 water molecules. Please
help me to do this.
Use a
On 1/05/2012 12:20 PM, cuong nguyen wrote:
Thanks,
I tried to add -maxsol 846 to the command and got the box with 846
water molecules. However, when I use VMD to visualize the box, these
molecules concentrate on 1/3 the box space. I do need the molecules to
spread out whole box.
So next
On 1/05/2012 6:49 PM, Shima Arasteh wrote:
Dear gmx users,
I've installed the gromacs version 4.5.5 on my laptop. But the version
of gromacs on the cluster, which I want to run MD, is 4.0. First of
all. is it possible that I use this one?
Yes, but you will run into differences, such as that
On 1/05/2012 4:58 PM, Banafsheh Mehrazma wrote:
Dear all;
I am wondering if we can use both disre and POSRES in .mdp file together?
Yes, this is a routine procedure for equilibrating while preserving an
initial structure for some reason.
To be more perspective, is it correct to add all
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
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
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
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 03/05/12, mu xiaojia muxiaojia2...@gmail.com 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
On 4/05/2012 1:10 AM, Albert wrote:
hello:
I've finished a MD job and I am wondering how can we extract
individual pdb from trajectories in Gromacs? each time I always get a
single pdb contains lots of snapshots.
See trjconv -h
Mark
--
gmx-users mailing listgmx-users@gromacs.org
out for computing it
myself, it is necessary to -pbc mol first, otherwise the molecules
might be broken for calculating scripts like matlab.
good to know this, thanks!
On Wed, May 2, 2012 at 8:03 PM, Mark Abraham mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au wrote:
On 03/05/12
On 3/05/2012 8:08 PM, Steven Neumann wrote:
Dear Gmx Users,
I run the simulation of protein-ligand complex. Then I extracted
coordinates for SMD - I want to pull away my ligand. I used to
topology from pevious simulation, so I removed water, ions from
topol.top as the size box will be
On 5/05/2012 1:47 AM, Elton Carvalho wrote:
Dear Gromacs users
I am currently preparing an RTP file to describe a polymer for use with MARTINI.
MARTINI does not include default bonded interactions, so all bonds,
angles and dihedrals must be explicitly defined in the topology file
or, in my
On 6/05/2012 7:10 AM, Andrew DeYoung wrote:
Hi,
I think that Gromacs has two parallelization algorithms as of version 4.5:
domain decomposition (the default) and particle decomposition.
For my research, I am using the particle decomposition algorithm. Thus, I
include the -pd switch when
On 6/05/2012 9:27 AM, Sai Kumar Ramadugu wrote:
Dear Gromacs Users,
I am trying to plot the Ryckaert-Bellemans energy for rotating the
chi1 dihedral of glutamate in protein.
I tried to change the ch1 dihedral from 0-360 degrees at increments of
1 degree and saved the pdbs. Then I used the
On 5/05/2012 11:39 PM, Marcelo Lopez wrote:
Hi, all, I'm still confused about how to set up 1-4 interaction tables
for tabulated non-bonding potentials when using the -tablep option in
mdrun.
The specific question is:
How must I specify the 1-4 interaction in those tables? How many
columns and
On 6/05/2012 9:08 PM, amit banerjee wrote:
Dear Gromacs Users,
I am trying to install gromacs 4.5.5
version in a CENTOS 5.4 machine with FFTW 3.3.1.
To do so, I have downloaded both the tar.gz files in root and tried to
install them as per the standard
On 7/05/2012 5:50 AM, Marcelo Lopez wrote:
For sure, this wouldn't happened if the information to run all the
Gromacs features were clearly explained in the place where should be:
the manual.
Life would be good if everything was perfect, but when you're relying on
free software provided by
Hi,
Please send requests for help to the gmx-users mailing list. I (and most
others there) are not available as private tutors.
Contrary to your assertion below, I've never run any simulations on
cytochrome P450. You probably need to name your iron atom more suitably
for your force field to
On 8/05/2012 5:19 AM, Elton Carvalho wrote:
Thank you for your reply, Mark,
On Sat, May 5, 2012 at 7:06 AM, Mark Abrahammark.abra...@anu.edu.au wrote:
Fundamentally, pdb2gmx is built for fine-grained force fields. I'd have
supposed Martini has some kind of builder program other than pdb2gmx,
On 10/05/2012 7:29 PM, Debayan Chakraborty wrote:
Dear Gromacs Users,
I want to simulate an organic dye in
a solvent ( such as aniline as DMA). I have already relaxed the
solvent around the dye in the equilibration run ( NPT) using position
restraints on the
On 14/05/2012 2:24 PM, mohan maruthi sena wrote:
Hi all,
I want to define a potential form and give it as input for
which i have seen manual ,thought gromacs table option is fine, i have
an example of generating 9-6 potential form , My question is how to
generate table.xvg, what is
On 14/05/2012 3:52 PM, Anirban wrote:
Hi ALL,
I am trying to simulate a membrane protein system using CHARMM36 FF on
GROAMCS4.5.5 on a parallel cluster running on MPI. The system consists
of arounf 1,17,000 atoms. The job runs fine on 5 nodes (5X12=120
cores) using mpirun and gives proper
On 14/05/2012 4:14 PM, bunty xy wrote:
Hello friends,
I am facing problem in using DSSP.
I want the DSSP Plot.The lattest binary of DSSP does not generate DSSP
Plot ,It generate .dssp file,which have values .But i want the DSSP
PLot.Please tell me the installation procedure and download link to
On 14/05/2012 4:18 PM, Anirban wrote:
On Mon, May 14, 2012 at 11:35 AM, Mark Abraham
mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote:
On 14/05/2012 3:52 PM, Anirban wrote:
Hi ALL,
I am trying to simulate a membrane protein system using CHARMM36
FF
On 11/05/2012 6:43 PM, Marzinek, Jan wrote:
Dear Gmx Users,
Many of you probably faced an error:
An input file contains a line longer than 4095 characters, while the
buffer passed to fgets2 has size 4095. The line starts with: '20s'
As I noted this error comes from the changes in the
On 14/05/2012 6:00 PM, Shima Arasteh wrote:
Thanks for your suggestions.
Now, I think that it's better to add the N atom of next residue to
the .pdb file and then add hydrogen atoms to its .mol2 format. Because
when I open formyl.pdb in chimera software and add hydrogens to it,
it becomes
On 14/05/2012 10:42 PM, Steven Neumann wrote:
Dear Gmx Users,
i run the implicit simulation with virtual sites on the hydrogen of my
protein. Now I want to extract coordinates and run another simulation
(in explicit solvent). Is there any way to remove those virtual sites
from my gro file as
On 15/05/2012 6:17 PM, David de Sancho wrote:
Dear all
I have been following Justin Lemkul's tutorial for the lysozyme
simulations
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html
I am using Gromacs 4.5.5.
My concern is with the energy conservation in the
On 15/05/2012 10:22 PM, neeru sharma wrote:
Dear gromacs users,
I am running steered MD simulation using Plumed plugin in gromacs for
a system consisting of Protein-Mg-GTP complex. I have to calculate the
distance of specific atoms with Mg and GTP.
While visualizing the trajectories using
On 15/05/2012 8:47 PM, Lara Bunte wrote:
Hi
After pdb2gmx I have two [ dihedrals ] sections in my topology. The first block
is empty, the second block is correct with my parameters.
An an example:
First block:
[ dihedrals ]
; aiajakal functc0c1
On 16/05/2012 4:53 AM, Lara Bunte wrote:
Hi
Is there some reason to believe you should not have dihedrals? That doesn't
make much physical sense.
I want and have dihedrals in my topology. I don't want an additional empty
dihedrals block in the topology. In my force field I gave impropers.
On 16/05/2012 3:43 PM, mohan maruthi sena wrote:
Hi all,
I use a user defined potential to describe non-bonded
interactions, as this excludes i, i+2,i+3. If i want to describe a
user defined potential for i,i+2,i+3,(i.e, 1-2,1-3) residues , how can
i give that in mdp file.
Doing
On 16/05/2012 12:28 PM, kevin wrote:
Hi, everyone.
It is my first use of Gromacs http://lammps.sandia.gov/ and I am
looking for a numerical scheme for one specific constrained SDE, the
constrain is a macroscopic one, i.e., overdamped Langevin(Brownian
dynamics) equations with an equality
On 16/05/2012 4:18 PM, priya thiyagarajan wrote:
Respected sir,
I am studying about micelle formation .. After setting box and adding
water i went for energy minimization and then went for nvt
equilibration for 1ns. when i visualized my nvt.pdb file, i found that
my protein comes together
On 16/05/2012 1:50 AM, daviddesancho wrote:
Thanks Florian and Mark for your replies.
I have run the simulation for longer (one order of magnitude longer, i.e. 1
ns) and what I get now is that the 'conserved energy' follows its drift
linearly. Now, of course, we are speaking about 1.2% drift/ns
On 16/05/2012 4:54 PM, Sathish wrote:
Dear all,
How to install DSSP in Gromacs 4.5.5.
i set environmental variable export DSSP=/usr/local/bin/dssp and
checked.
I have refereed many posts related to dssp issue and tried with new
and old dssp executable but confused.
While running i got
precision)
Segmentation fault (core dumped)
[root@localhost sathish]#
Am not clear to understand this problem. help me
--
--
Regards,
N. Sathishkumar,
mailto:sath...@khu.ac.kr
On Wed, May 16, 2012 at 4:02 PM, Mark Abraham mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au wrote
On 16/05/2012 5:50 PM, Lara Bunte wrote:
Hi
If I use pdb2gmx -f mymol.pdb -water tip3p (CHARMM27 force field) I got
warnings like this:
Making bonds...
Warning: Long Bond (1-2 = 0.261872 nm)
Warning: Long Bond (2-4 = 0.267812 nm)
Warning: Long Bond (6-4 = 0.260531 nm)
and so on
For
On 18/05/2012 2:52 AM, francesco oteri wrote:
Dear gromacs users,
I am trying to port a set of charm parameter in gromacs.
I am using the script convert_charmm_to_gromacs.pl
http://convert_charmm_to_gromacs.pl contained in the
file charmm_to_gromacs.tgz
:* Mark Abraham mailto:mark.abra...@anu.edu.au
*Date:* 2012-05-16 13:57
*To:* Discussion list for GROMACS users mailto:gmx-users@gromacs.org
*Subject:* Re: [gmx-users] What is the subroutine for SHAKE or RATTLE?
Thanks.
On 16/05/2012 12:28 PM, kevin wrote:
Hi, everyone.
It is my first use of Gromacs
On 17/05/2012 11:47 PM, Lara Bunte wrote:
Hello
After
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
I got the error:
Incorrect number of parameters - found 2, expected 4 or 4 for U-B.
I thought that this could be an inconsistency be declaring the functions, but
in my topology
On 18/05/2012 4:43 PM, Seera Suryanarayana wrote:
Dear all,
While i am running gromacs software i am getting following
error.Let me know how to over come that error
Fatal error:
number of coordinates in coordinate file (208L_ion.gro, 62283)
does not match topology
On 18/05/2012 4:50 PM, Seera Suryanarayana wrote:
Dear all,
While i am running gromacs software i am getting following
error.Let me know that error how to over come.
Fatal error:
Residue 'CSD' not found in residue topology database
Please search for your own answers before
On 18/05/2012 6:14 AM, mohan maruthi sena wrote:
Hi all,
I have used a user define potential to describe attractive
potential beyond i and i+3 atoms(similar to lLJ). If i want to
describe repulsive interactions with in i and i+3 , how can i do it in
gromacs? can anyone suggest me a
On 23/05/2012 1:24 AM, Tomek Wlodarski wrote:
Hi,
-s before -deffnm works, now after starting once more REMD from
the scratch I can do restart.
I use
mpirun mdrun_mpi -multi $nrepls -deffnm ${name}_sim $npme -cpi
${name}_sim -append
and it Just Works with 4.5.5.
Mark
Thanks.
Best
On 23/05/2012 8:36 AM, Tom Dupree wrote:
Greetings all,
I now realise I asked too many questions with that one post.
I would like to check that mdrun -rerun can be used to do single point energy
calculations on the co-ordinate frames from my trajectory using a different
electrostatic model by
On 23/05/2012 4:20 AM, Muyi Xu wrote:
Hello
I am trying to change a crystal structure(wih amc or cif format) into
a .pdb format; but gromacs gives me input/output error; which means my
input file has the wrong format. Do u have any suggestions how to
convert or what software to use?
Perhaps
On 23/05/2012 6:42 PM, Alan wrote:
Thanks Justin, you were right. In the end gmxdump helped to clear some
doubts but I wished it would be less painfully.
One useful approach is to simplify the system as much as possible before
producing the .tpr and using gmxdump. The necessary
On 25/05/2012 7:44 PM, Julian Mondon-Garrec wrote:
Hi all,
I am trying to get the electrostatic forces acting on each atom as a
function of time. I have checked the list and all the suggestions are
based on rerunning the simulation. Is there not an easy way to print
these forces on the fly ?
On 25/05/2012 7:52 PM, Steven Neumann wrote:
Dear Gmx Users,
My system is made of 3 proteins. As I want to use distance restraints
dynamics between atoms belonging to each of them I have to produce
topoloy with one moleculetype. I used pdb2gmx -chainsep interactive (I
used merge: yes).
On 28/05/2012 7:48 AM, Justin A. Lemkul wrote:
On 5/27/12 5:29 PM, Igor Druz wrote:
I would like to save disk space and write only protein coordinates using
xtc-grps, but preserve the same precision as in trr file. What value of
xtc-precision should be used to achieve this?
Why not write
On 28/05/2012 8:14 AM, Igor Druz wrote:
/ You need to choose a large .xtc precision, or use nstxout and filter the
group
// afterwards./
/
/
/I tried xtc-precision=100. This gives the same result as the default
value//xtc-precision=1000./
That seems highly unlikely. Can you demonstrate
On 29/05/2012 3:09 PM, a a wrote:
Dear Sir/Madam,
Follow the steps below, I have installed fftw library and gromacs as a
root.
(1) tar -xzvf fftw-3.0.1.tar.gz
(2) cd fftw-3.0.1
(3) ./configure --enable-float --enable-threads --enable-shared
Here you enabled threads for fftw, which is not
On 29/05/2012 3:21 PM, James Starlight wrote:
Justin,
the main problem is the my simulation in nvt ensemble :) I understand
that density is constant in that conditions but I'd like to find way
to check this values for different components of my system.
AFAIK, there's no easy way to do that
On 27/05/2012 2:00 AM, Andrew DeYoung wrote:
Hi,
It is possible to compute the number density using g_density, with the
switch -dens number. Do you know if this is the number density of
molecules? Or is it the number density of atoms?
I'd expect atoms, but you should be able to test for
not be applicable. If CHARMM36 uses more
than one kind of improper dihedral, then I would not expect the script
to function correctly in this regard. You would need to modify the
script or its output.
Mark
Francesco
2012/5/18 Mark Abraham mark.abra...@anu.edu.au
mailto:mark.abra
On 29/05/2012 6:37 PM, a a wrote:
Dear Sir/Madam,
Thanks for the insightful comments from the experts.Follows the
steps, I found the source of error:
This what I have done:
In the following directory /home/softwares/fftw-3.0.1:
On 30/05/2012 1:50 AM, a a wrote:
Dear Mark,
I have overlook it. Sorry.
I have already added the following two sentences in .bashrc file in my
home directory (when I login as user).
export CPPFLAGS=-I/home/softwares/fftw301/include
export LDFLAGS=-L/home/softwares/fftw301/lib
Should I
On 30/05/2012 4:45 PM, oguz gurbulak wrote:
Dear All,
I want to ask some questions about trajectory analysis. I have some md
simulation output files that includes coordinate, force and velocity
information. And these files are huge ( more than 5 GB ) . Could you
please recommend a free text
On 30/05/2012 5:33 PM, MD wrote:
Hi All,
I have to use the long range correction for VDW, in fact i used
cut-off=1.4 nm for calculation of surface tension of TIP4P/2005, we
can get 65 dyn. The .mdp i used are as follow, I really need to know
how to get a surface tension of 69.5 dyn for
On 30/05/2012 7:24 PM, MD wrote:
Yes, i try to get a surface tension of 69 dyn, but i can only get 65
at present.
Yes, i tried some arbitrary choices. I do not know what is the correct
.mdp for me to get a surface tension of 69. May be for this version,
it does not include this function
On 30/05/2012 9:30 PM, ramaraju801 wrote:
hi,
recently while working on gromacs i came across this error There is
a dangling bond at at least one of the terminal ends and the force field
does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb
file. i tried to edit .tdb file
On 30/05/2012 9:42 PM, Stephen Cox wrote:
Hi Justin,
Thanks for getting back and posting the links.
On 5/29/12 6:22 AM, Stephen Cox wrote:
Hi,
I'm running a number of energy minimizations on a clathrate
supercell and I get
quite significantly different values for
On 31/05/2012 4:42 PM, Acoot Brett wrote:
Dear All,
The value of the energy of the hydrogen bond has relation with
distance and angle of the hydrogen bond related atoms. As for in the
simulation process, the distance and angle of the hydrogen bond
related atoms may change continuously. Will
On 31/05/2012 4:13 PM, ramaraju801 wrote:
when i ran gromacs to produce topology file for a nucleotide sequence it is
showing the above error saying There is a dangling bond at at least one of
the terminal ends and the force field does not provide terminal entries or
files. Edit a .n.tdb
On 31/05/2012 11:24 AM, Andrew DeYoung wrote:
Hi,
I have a system in a slab geometry. A surface exists at z = 0; many
hydrogens protrude from the surface, and these hydrogens are mostly (but not
precisely) immobile. Above the surface, there is liquid, including the
anion BF4- (tetrahedral
over which you can integrate.
Mark
Cheers,
Acoot
*From:* Mark Abraham mark.abra...@anu.edu.au
*To:* Discussion list for GROMACS users gmx-users@gromacs.org
*Sent:* Thursday, 31 May 2012 4:48 PM
*Subject:* Re: [gmx-users
On 31/05/2012 9:11 PM, Ignacio Fernández Galván wrote:
Hi all,
There must be something I don't fully understand, by running grompp on a
system, I get this:
Estimate for the relative computational load of the PME mesh part: 0.32
Good, that's approximately 1/3, or a 2:1 PP:PME ratio, which
On 31/05/2012 9:37 PM, Subramaniam Boopathi wrote:
how to assign charge and charge group number when new residue as being
added to the existing amino acid rtp file
Read about the file format in the manual.
Mark
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gmx-users mailing listgmx-users@gromacs.org
On 31/05/2012 10:17 PM, vidhya sankar wrote:
Dear justin
Thank you for your previous reply
Now i am trying to run the parallel gromacs simulation (gromacs 4.5.5)
first of all i have successfully installed debain package of
gromacs-openmpi
for that i have configured and compiled
On 1/06/2012 12:18 AM, MD wrote:
Hi All,
I really need to know how to apply long range LJ correction to
calculate surface tension of TIP4P/2005 water. I can get 65 dyn even i
use vdw cut-off = 1.4 nm, but from the reference people can get 69 dyn.
I included the LJ Long range LJ correction
On 2/06/2012 1:11 PM, Klniu wrote:
Dear Gromacs users,
I am doing a membrane simulation. The system are two layers composed by
surfactants. other molecule are decane and water. The system like this:
decane
---
surfactant
---
water
On 2/06/2012 7:10 PM, xi zhao wrote:
Dear gmx-users:
When I try to simulation a system: protein + ligand molecule using the
Implicit Solvent method. the parameters of Ligand were produced by
acpype, but when grompped, the appeared
Velocities were taken from a Maxwell distribution at 300 K
GB
On 3/06/2012 11:03 PM, xi zhao wrote:
in fact, the pdb2gmx still hang. I modified the atomtypes.atp ,
aminoacids.rtp , ffbonded.itp, ffnonbonded.itp ,
aminoacids.hdb, residuetypes.dat4
,morever, now the pdb2gmx_d even does not the standard protein structure.
So clearly you have broken the
On 4/06/2012 5:00 PM, Acoot Brett wrote:
Dear All,
Will you please tell me how to rename the C-terminal residue atom OXT
so that the OXT oxygen can be recognized by MOLMOL?
You'd have to read the MOLMOL documentation. But start with O - making
sure you preserve the file format correctly,
On 4/06/2012 5:05 PM, Seera Suryanarayana wrote:
Dear all gromacs users,
While i am running pdb2gmx commond i
am getting following error.
Fatal error:
There were 22 missing atoms in molecule Protein_chain_A, if you want
to use
this incomplete topology.
I
On 4/06/2012 3:46 AM, ramesh cheerla wrote:
Dear Gromacs experts,
I am planing to use tabulated
potentials for dihedral functional form Summn over 'n' 0.5*K [ ( Cos
n(phi-phi0)] , Here 1= n = 3 . I have three different K values (i.e
K1,K2,K3 ) one for each
On 4/06/2012 6:18 PM, Wayne Chen wrote:
Hi,
I'm a student at National Taiwan University doing research on protein-ligand
interactions using MD simulations with GROMACS (version 4.5.3). In our
simulations, we placed a protein (group A) and a ligand (group B) in a box
under periodic boundary
On 5/06/2012 12:08 AM, Laurence Leherte wrote:
Dear Gromacs users,
I am using the Amber99 FF in MD simulations of peptides (and
proteins). In a first stage to the design a different charge
distribution, most of the atomic charges were set equal to zero (i.e.,
all charges but the C and O
On 5/06/2012 9:11 AM, Peter C. Lai wrote:
The quick and dirty way is to post-patch Makefile in src/tools.
I think patching the appropriate Makefile.in is sufficient for configure to
pick up and automake into Makefile if all you need to do is append a make
target.
As to your previous question,
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