On 7/15/12 1:59 PM, Andrew DeYoung wrote:
Hi,
I have been not been able to access http://www.gromacs.org/ today. Has
anyone else experienced this? I received the following error message on
both Google Chrome and Mozilla Firefox:
--
Site settings could not be loaded
We were unable to locate
On 7/16/12 5:36 AM, Raj wrote:
Hi all,
It may be naive but I would like to get some clear explanation in SMD ( COM
pulling) reg. The question is, Before performing the COM-pulling (incase of
protein ligand complex) do we need to position restrain the ligand using
genrestr and then add the
On 7/16/12 7:19 AM, Inon Sharony wrote:
Good afternoon.
g_traj has the option to output position coordinates (-ox) OR velocity
coordinates (-ox) from an input trajectory file. The former can even be
output to a trajectory file format, trr/trj/cpt (-oxt). I would like to
On 7/16/12 10:25 AM, Giovani Mancini wrote:
Dear Gromacs users,
I just read the tutorial by Justin Lemkul about umbrella sampling simulations
along z-axis. My question is whether we need cylindrical confinement of the
molecule that is pulling away from a reference molecule.
Thanks
On 7/16/12 10:39 AM, Giovani Mancini wrote:
Dear Justin,
Thank you very much for your immediate response to my e-mail.
I am trying to conduct umbrella sampling simulations of a molecule into a lipid
bilayer (DLPC) along the z-axis. As a reference, I used your tutorial which is
On 7/16/12 10:59 AM, Andrew DeYoung wrote:
Hi,
If you have time, I'm wondering if you can please help me to think through a
problem that I seem to be having with g_hbond. I am looking for a way to
list the _individual_ hydrogen bonds as a function of time, by indices --
more than just
On 7/16/12 5:42 PM, Manikam Sadasivam Saravanan wrote:
Hi,
I am a new user to Gromacs, just started exploring it since 3 months, Thanks
to Justin, In-fact i learned a lot form his tutorial using KALP protein in
dppc.
Currently I am working with simulation of Membrane protein in a popc
On 7/17/12 4:05 AM, J Peterson wrote:
Hi Justin,
I have the following Notes during NPT equilibration.
NOTE 1 [file pr_NPT.mdp]:
nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
http://manual.gromacs.org/online/mdp_opt.html#out
On 7/17/12 7:16 AM, Markus Kaukonen wrote:
Dear All,
I rephrase my question (for the original see below).
Is there any (easy) way to give gromacs (mdrun -rerun) accurate coordinates for
a single point calculation (to get accurate energy and forces)?
The accuracy of .pdb and .gro formats is
On 7/17/12 12:51 PM, Markus Kaukonen wrote:
Convert the .g96 file to .trr format. Double precision may be necessary and
will certainly give the greatest possible accuracy.
-Justin
I try
trjconv -f gromacs.g96 -o test.trr
and get
Program trjconv, VERSION 4.5.5
Source code file:
On 7/17/12 4:37 PM, Alex Marshall wrote:
Hi all,
I have a system that consists of two distinct reservoirs filled with
water+NaCl connected by a CNT. I want to measure the average number of
hydrogen bonds per water in each reservoir as a function of time, but
my current workflow for this is
On 7/17/12 4:57 PM, Andrew DeYoung wrote:
Hi Justin,
I am just curious, do you have experience writing such a shell script to
iterate over the index files (one per frame)? I am just curious, because I
have been trying this, and I have found it very difficult to do using bash.
Do you use a
is the problem solved then?
-Justin
On Tue, Jul 17, 2012 at 12:03 AM, Justin Lemkul jalem...@vt.edu wrote:
On 7/16/12 5:42 PM, Manikam Sadasivam Saravanan wrote:
Hi,
I am a new user to Gromacs, just started exploring it since 3 months,
Thanks
to Justin, In-fact i learned a lot form his
On 7/18/12 5:58 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I want to use pdb2gmx for my protein.
My protein has a ACE cap at one termini. And I looked it up in the
aminoacids.rtp file and there is also a ACE entry.
But still I get an error when using pdb2gmx
my
On 7/18/12 3:03 AM, joja...@jgypk.u-szeged.hu wrote:
Hi,
Check this article:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0032131
HTH Balazs
In addition, it is important to realize that a single trajectory represents one
possible outcome, and no matter how long it is,
On Wed, Jul 18, 2012 at 12:08 PM, Justin Lemkul jalem...@vt.edu wrote:
On 7/18/12 5:57 AM, Manikam Sadasivam Saravanan wrote:
Thanks for the message, I have a .pdb containing my membrane protein
inside the leaflet of popc bilayer, so i wanted to remove the
interacting lipid molecules, hence i
On 7/18/12 7:35 AM, James Starlight wrote:
Dear Gromacs Users!
I have two trajectories with removed PBC which was done by the below command.
trjconv -s MD_B2ar_WP_3.tpr -f MD_B2ar_WP_3.trr -o md_noPBC.xtc -pbc
mol -ur compact
Both of that trajectories are of the same system- when one
On 7/18/12 7:48 AM, Manikam Sadasivam Saravanan wrote:
my command to inflate was - perl inflategro.pl protein_popc.gro 4 POPC
14 system_inflated.gro 5 area.dat
my gro file looks like,
membrane protein in POPC 121-310KWITNOIONS
59522
1SER N1 -2.092 -1.832 -1.359
1SER
On 7/18/12 8:24 AM, nikhil gadewal wrote:
Dear users,
I am getting the problem in reading full .xtc file. The simulation time is 200
ns. But while giving command
./g_hbond -f dna_pro_whole_nojump_cent.xtc -s sys2.tpr -num Pro_H2A2.xvg
I am getting below error. The .xtc file is reading
On 7/18/12 9:34 AM, James Starlight wrote:
Justin
thanks for advise
I've used the bellow command for both trajectory
trjcat -f md_noPBC.xtc md_noPBC_GO.xtc -tu ps -o merged_noPBC.xtc
but resulted merged_noPBC.xtc consist of data from only second
trajectory although in the log file both
On 7/18/12 2:41 PM, kaushik lakkaraju wrote:
Hello gromacs users,
I am trying to use pdb2gmx to bring my crystal structure into gromacs
environment. The protein in the crystal has glycosidic linkages. In
charmm, I could attach these carbohydrate structures using PATCH
command.
What is the
On 7/18/12 4:57 PM, zifeng li wrote:
Dear Gromacs users,
I am calculating hydrogen bonds between polymer and water using
Gromacs 4.5.4 and opls-AA force field. Our goal is to extract
coordinates of atoms which form hydrogen bond at each frame.
1. The way I do it now is iterating following
On 7/18/12 5:37 PM, Rajat Desikan wrote:
Hi all...
I heard that gromos 54a7 ff is much better for simulations than 53a6. i have
a membrane protein system. To simulate it, should I include the berger lipid
parameters manually as shown in justin Lemkul's membrane protein tutorial?
The Berger
On 7/18/12 5:51 PM, Rajat Desikan wrote:
54A7 also introduced changes to the Gromos96 lipid parameters
How will this change my inclusion of the berger lipid parameters? Any thing
that I should pay special attention to? Are there other lipid parameters
more compatible?
There are better force
On 7/18/12 6:13 PM, Rajat Desikan wrote:
Thanks for the quick and detailed replies Justin :) This helped clear some
doubts I had.
I thought all Charmm ff were compatible in Gromacs? Which Charmm ff were you
referring to?
CHARMM force fields are largely just sequential additions and
On 7/18/12 6:57 PM, Thomas Piggot wrote:
Hi,
Justin, I am interested by your comments regarding the CHARMM lipids. In
particular can you elaborate as to why you think that the CHARMM lipids are
better than the united-atom ones (such as Berger and several GROMOS variants).
I think there's
On 7/19/12 5:00 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I want to add protonation states to my protein with pdb2gmx.
I now that there are the options:
-lys -arg -asp -glu -his
to do this.
But was is about the cystein. How can I protonate this one?
Is there also
On 7/19/12 6:17 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
thank you for your answer.
I already tried the -ss command but nothing happens. The program just
writes the topology file but it does not ask me anything. My command was:
pdb2gmx -f protOnly.pdb -o 3m71.gro -p
On 7/19/12 6:28 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
There is only one Cystein:
ATOM 1797 N CYS A 211 10.568 1.888 4.891 1.00 1.00
ATOM 1798 CA CYS A 211 11.782 1.312 5.391 1.00 1.00
ATOM 1799 CB CYS A 211 12.968 1.606 4.452
On 7/19/12 8:06 AM, mohammad agha wrote:
Dear Gromacs Users,
I have several questions about g_clustsize, Please help me.
I have several micelles in my system and I want to calculate: the number of
monomers in micelles and cluster number and monomer number during the time of
simulation,
On 7/19/12 9:42 AM, mohammad agha wrote:
Dear Justin,
Thank you very much from your response.
according you said I should set -cut with less than 0.7, but this doesn't
answer me!
I didn't say that, but your results are completely consistent with what I said
about how g_clustsize is
On 7/20/12 6:46 AM, radhika jaswal wrote:
Dear all,
I did NVT simulations of a number of molecules with double bond. But when i
analysed the results i realised that double bond has been converted to single
bond and sp2 hybridisation has also changed to sp3. I was doing with all bonds
On 7/20/12 2:00 PM, Debashis Sahu wrote:
Dear all
I used Gromacs 4.5 for thio-Urea molecule in OPLS-AA force
field, but in grompp step I got an error as follows:
---
Back Off! I just backed up
On 7/20/12 2:26 PM, Debashis Sahu wrote:
Dear user,
I have used this RB dihedral for thiourea in
ff-bonded.itp file, which is the error line mentioning below:
dih_THI_H_N_C_S 23.1 -2.1
-21.0 0.0 0.0 0.0
On 7/20/12 3:50 PM, Katie Maerzke wrote:
Hi all -
I am trying to set up a topology file for an ionic liquid force field not
included in Gromacs. How do I know which dihedral type corresponds to which
functional form? For the angular potentials, I assume type 1 is harmonic - is
this
On 7/20/12 11:47 PM, Mark Abraham wrote:
On 20/07/2012 11:32 PM, francesco oteri wrote:
Dear gromacs users (and eventually developers too),
I am trying to debug gromacs and on the gromacs website
http://www.gromacs.org/Developer_Zone/Programming_Guide/Programmer's_Guide#local_index
It is
On 7/21/12 2:13 AM, Mark Abraham wrote:
On 21/07/2012 3:44 PM, radhika jaswal wrote:
When replying to a digest, do change the subject to something useful, and do not
include the entire digest in your email. People have better things to do than
scroll through lots of text to find the relevant
On 7/23/12 2:39 AM, tarak karmakar wrote:
Dear All,
In my simulation I want to fix the S=O bond length of SO2, but the
angle has to be kept flexible. So I search for the distance restraints
in gromacs mailing list and
accordingly I have incorporated the distant_restraints block in the
On 7/23/12 5:31 AM, J Peterson wrote:
Hi Justin,
Thanks for all your help to get me through membrane simulations.
I've a problem to be solved. I need a long and thick membrane to simulate a
big protein. The longest bilayer that I can download from Tieleman's website
is 64 molecules long.
On 7/23/12 7:53 AM, J Peterson wrote:
Thank you so much for that, Justin.
Now I could expand the bilayer.
I've another query. My protein has a small N-terminal portion embedded in
the membrane, I would like to insert only this part into the membrane during
'packing the lipid around the
23, 2012 at 4:11 PM, Justin Lemkul jalem...@vt.edu wrote:
On 7/23/12 2:39 AM, tarak karmakar wrote:
Dear All,
In my simulation I want to fix the S=O bond length of SO2, but the
angle has to be kept flexible. So I search for the distance restraints
in gromacs mailing list and
accordingly I
On 7/23/12 9:54 AM, Christian Blouin wrote:
Hello,
I have been running a simple simulation where I replace 150
water molecules in a waterbox with a lipid called DPC to create
micelles. This simulation is working fine and I'm getting decent
micelles fairly quickly. I am now trying to
On 7/23/12 12:32 PM, SatyaK wrote:
Hello All,
I have an issue with converting a .dat file into GRO format and viewing it
in VMD. Say, we have {x, y,z} ={0,0,1} in A.
Converted GRO file (in nm): 171OHX OW 5000 0 01000.000
The Z coordinate has 8 places which is apt as per
On 7/23/12 12:53 PM, SatyaK wrote:
Thanks for the reply. In fact, I had followed the fixed format of Gromacs
during the conversion. Below is the sample data, where I have just the
{X,Y,Z}:
2171OHX OW 5231 -0.543 -2.5801000.000
2171OHXHW1 5232 -0.510 -2.5471000.110
Z
On 7/23/12 2:47 PM, Debashis Sahu wrote:
Dear all user,
I'm a gromacs beginner and have a quick question.
Can anyone tell me about the .hdb file description, e.g. '8' indictes
no.of kind of hydrogen, ARG is residue name, after that 1st column
indicates the no. of hydrogens
On 7/24/12 2:49 AM, J Peterson wrote:
Thanks for that comment.
I've another query during inflating step in Justin's tutorial.
In my case, during the inflation, 4 lipids from the upper and 2 lipids from
the lower leaflets were removed.
Would there be a problem in this sort non-uniform
On 7/24/12 6:13 AM, Nidhi Jatana wrote:
Dear Sir/Madam
I am running simulations on a membrane protein using Desmond and I
want to calculate area per lipid for the entire trajectory. I can
convert the trajectories to those of Gromacs using VMD. What else do I
need in order to calculate area per
On 7/24/12 2:34 AM, mohammad agha wrote:
Dear Gromacs Users,
I don't know what is the quantity of -cut in g_clustsize for different systems,
exactly!
It is the cutoff value that determines if two molecules are in the same cluster.
If atoms in different molecules have a distance less
On 7/24/12 8:18 AM, SatyaK wrote:
Thanks Justin for your reply.
Going by the Gromacs file format: position (in nm, x y z in 3 columns,
each 8 positions with 3 decimal places)
It is not clear to me as to how many digits before the decimal point can a
coordinate column accepts in the
Please keep the discussion on the gmx-users list.
On 7/24/12 8:31 AM, mohammad agha wrote:
Dear Justin,
Thank you very much from your response, is there only RDF calculations to reach
cutoff value?
RDF is one possible method to find out how closely atoms or molecules are
interacting,
On 7/24/12 10:14 AM, neme...@pharm.u-szeged.hu wrote:
I have to simulate a G0 PAMAM dendrimer, functionalized on the 4 hands
with peptide oligomers. I have succesfully generated the .itp file needed,
and have run some simulation. The same applies to the peptide. However i
run into problems
On 7/24/12 10:39 AM, neme...@pharm.u-szeged.hu wrote:
Thank you for the fast answer, i will do that then. Do i have to close
this thread, or it will fade by itself?
Nothing fades, everything stays archived :) But if the issue is closed, simply
stop replying to the thread, and ask any new
On 7/25/12 7:06 AM, Ali Alizadeh wrote:
Dear All users:
How to generated a .gro file for a special molecules?
For example:
Tutorial 4: Biphasic Systems
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html
On 7/25/12 7:06 AM, akn wrote:
Dear gmx users,
I want to calculate the center of mass of each molecule in the system all
through the simulation time.
When I used g_traj -f traj.xtc -s topol.tpr -n index.ndx -ox coord.xvg
-com'' command, I obtained the center of mass of the system
I tried
On 7/25/12 7:30 AM, Shima Arasteh wrote:
Hi,
The force field which I am using is CHARMM36.
I added some new atom types to the atomtypes.atp . Then I need to change the
nonbonded.itp file. Are the atom names are used in .itp files? So how I find a
last-defined atom types in the .itp
On 7/25/12 7:58 AM, Shima Arasteh wrote:
Some time ago I defined a new residue and after running grompp I got an error
as there are some interactions assigned multiple times. Then I decided to
duplicate the atoms involved in that residue to avoid this error.
That error usually
On 7/25/12 2:32 PM, Ramon Garduno wrote:
Dear gmx friends:
We are modeling a solvated hydroxyapatite(HAP)-protein complex. We have
minimized and equilibrated this system to 300K under NVT.
The odd behavior is observed when we start an NPT simulation. In the very
first ps we observed that the
On 7/26/12 6:07 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
On 26/07/2012 6:47 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Ho,
first I minimize my structure. This is the corresponding mdp file:
define = -DPOSRES
integrator = steep
emtol
On 7/26/12 3:55 AM, neeru sharma wrote:
Dear Gromacs users,
I have a query regarding the number of bins used in wham analysis.
If I have performed by simulations over 15 umbrellas (15 different
staring structures), what should be the ideal number of bins to
perform wham analysis? Does it
On 7/26/12 6:23 AM, akn wrote:
Dear Gromacs users,
Is it easily possible to calculate the number of H-bonds per molecule across
the box by using gromacs? If it is, how can I do this?
One would have to use g_select on a particular region of the box (simple
coordinate boundaries) to work
On 7/26/12 7:06 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
On 7/26/12 6:07 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
On 26/07/2012 6:47 PM, reising...@rostlab.informatik.tu-muenchen.de
wrote:
Ho,
first I minimize my structure. This is the corresponding mdp file:
On 7/26/12 7:52 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
On 7/26/12 7:06 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
On 7/26/12 6:07 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
On 26/07/2012 6:47 PM, reising...@rostlab.informatik.tu-muenchen.de
On 7/26/12 8:05 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hmm, okey. Thank you.
So all in all what I did was correct and it should only minimize the
hydrogen atoms and not the rest of the protein nor the membrane. Right?
To sum up:
1. The Protein-H group does indeed contain
On 7/26/12 8:30 AM, tarak karmakar wrote:
Dear All,
While running minimization I imposed the the condition for the
minimization as to be converged only at Fmax 10 . But I got the
following
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested
On 7/26/12 9:48 AM, niaz poorgholami wrote:
Dear Mark
thank you for your concern.when I tried the g_sgangle program
it gave me
Fatal error:
Something wrong with contents of index file.
the index file was the one I used during the simulation and I made that
with this command:
make_ndx -f em.gro
On 7/26/12 9:59 PM, Andrew DeYoung wrote:
Hi,
I would like to extend a run. I ran a 10 ns simulation, and I would like to
run the simulation for an additional 10 ns. Normally I would do this with
the following two commands:
tpbconv -s topol_old.tpr -o topol_new.tpr -extend 1
mdrun -cpi
On 7/27/12 10:58 AM, Shima Arasteh wrote:
Thanks dear Mark for your reply.
It was just a simple question, liked to hear answers from the one who knows
more about the simulation packages more than me. Again thanks dear Mark.
In my own, I've only worked with GROMACS and don't have any
On 7/27/12 8:50 AM, J Peterson wrote:
Hi Justin, Thanks for that information.
I also would like to confirm with you that should I combine my metal ion too
while I combine Protein and POPC into Protein_POPC group to be used in COMM
removal? So that I will have a group Protein_HEM_POPC.
With
On 7/27/12 11:31 AM, Andrew DeYoung wrote:
Hi,
Thanks, Justin! Is it possible to set the start time as t = 10 ns instead
of t = 0? When I pass the checkpoint to grompp with -t, the simulation
starts at t =0 by default. Is there a way to change this, such that I will
be able to easily
On 7/27/12 12:50 PM, yousef nademi wrote:
hi everybody
i want to calculate the P_N orientation of dppc lipid bilayer but in g_angle
index file shoud have at least 3 atom but in P_N vector i want to define 2 atom
is there anyone know what should i do?
g_sgangle with the -z option
to write a simple histogram program.
-Justin
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: yousef nademi yousef_nad...@yahoo.com; Discussion list for GROMACS users
gmx-users@gromacs.org
Cc:
Sent: Friday, July 27, 2012 9:57 AM
Subject: Re: [gmx-users] p_N head group
.
-Justin
Thanks in advance
Cheers,
Shima
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc:
Sent: Wednesday, July 25, 2012 4:37 PM
Subject: Re: [gmx-users] adding a new atom type
On 7/25/12 7:58 AM, Shima Arasteh wrote
On 7/27/12 9:55 PM, Ladasky wrote:
Hello Mark,
Thanks for your reply. It has taken me several days to make some progress
on my issues. I'm just going to address one specific point in this post.
Mark Abraham wrote
On 19/07/2012 6:52 PM, Ladasky wrote:
I once used the -deuterate option
1000 1000
#endif
; Include topology for ions
#include gromos53a6_HAP.ff/ions.itp
[ system ]
; Name
newbox-pep2 in water
[ molecules ]
; Compound#mols
HAP1
Looking forward to your comments...
Cheers,
Ramon
On Wed, 25 Jul 2012 15:10:43 -0400, Justin Lemkul
On 7/28/12 7:34 AM, Shima Arasteh wrote:
Hi all,
My system has got BLOWING UP . I followed the protocol in
http://www.gromacs.org/Documentation/Terminology/Blowing_Up and got as below:
Step 1: If the crash is happening relatively early (within a few steps), set
nstxout (or nstxtcout)
On 7/28/12 5:28 AM, yousef nademi wrote:
hi gromacs users and especially Dr. Justine
in using the g_sgangle i have to define index file contain multiple of two
defining all the P and N atoms but after executing the g_sgangle i get the
message:something wrong with contents of index file
after
On 7/28/12 2:47 PM, Shima Arasteh wrote:
Dear Mark, Thanks for your suggestions.
Atom 1 is the C which is expected to connect to the H ( atom 18) . Atom 5 is
tha CA of the next resisue ( Valine), the bond 18-5 is not expected at all!
However I see this pair in the [pairs] section of
On 7/28/12 1:49 PM, tarak karmakar wrote:
Dear All ,
I wanted to keep all the molecules other than water fixed [
positiion restraints]. So for that I have performed short NVT
[simulation with DEPOSRE] after minimization, but while seeing the
movie of the trajectory in VMD I see the
On 7/28/12 1:43 PM, tarak karmakar wrote:
Dear All,
The protein with which I'm working with, contains Zn metal and it
has tetrahedral coordination site. There are HISTIDINE side chains
within distance ~ 2.3 to 2.4 . So my questions are as follows
(1) In that distance range there is no
On 7/29/12 3:30 AM, James Starlight wrote:
Dear Gromacs Users!
I want to analyze protein-ligand polar interactions by means of g_hbond utility
In particular I want to obtain some map wich include information
aabout dynamics of the h bonds occurence between defined polar groups
of the
On 7/29/12 9:39 AM, vidhya sankar wrote:
Dear Justin Thank you for your previous reply
When i run the .pdb2gmx_d -f 1OG2O.pdb -o 1OG2O.gro -p 1OG2O.top -renum
It runs successfully. But i have on issue. My PDB contains HIS residues in
both chain A and B I have selected
GROMOS96 53a6
On 7/30/12 5:55 AM, Za Pour wrote:
Dear gmx users
I am trying to analyze the results of my simulations. a system
including one CNT+12 small molecules.I would like to know the distribution
of angles formed by these 12 small molecules around CNT.I have found from
manual that
g_sgangle may do
On 7/30/12 1:07 PM, vidhya sankar wrote:
Dear Justin, Thank you for your Previous Reply.
I have got the following Error in EM using steepest
Descent method in gromacs
Warning: 1-4 interaction between 4728 and 4733 at distance 3.030 which is
larger than the 1-4 table
On 7/30/12 5:15 PM, sai nitin wrote:
Dear all,
I recently started protein ligand simulation using gromacs my aim is
to calculate binding free energies after simulations...I adapted
justin tutorial
and done 10 ns MD simulations using CHARMM FF and now going through
LIE (Linear Interaction
On 7/31/12 7:48 AM, Ali Alizadeh wrote:
Dear All usres:
I am trying to do a simple system that contains 4 molecules ethane and
MD run using GROMACS. I build my .pdb file by using Avogadro software
. Afterwards, I try to generate the topology and .gro file using
pdb2gmx program and it
On 7/31/12 10:14 AM, Laura Kingsley wrote:
Hello,
I've just switched from using Gromacs version 4.0.5 to 4.5.5, and I'm having an
issue with make_ndx. Using the old version I have a single group showing up for
each odd residue, eg JJJ shows up once as group 16 for example. When I use the
new
On 7/31/12 5:21 PM, Shima Arasteh wrote:
Thanks for dear Mark's suggestions.
What's the typical solution to fix such errors of grompp?
I don't have any idea to do what, so erased the lines defined in output of
grompp, then I went through the NVT equilibrium, it didn't stop by multiple
On 7/31/12 7:46 PM, Shima Arasteh wrote:
But If I want to use acetyl instead of formyl, then what about the chemical
activity of the formyl located in N-terminus?
The protein that I will put in the bilayer is composed of 2 monomers . The
monomers form a dimer from the N-terminus, the
All,
Inspired by recent discussions regarding virtual sites and linear molecules
(which seems to be a fairly common topic), I have created a new tutorial for
creating such molecules:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html
It is also linked
On 8/2/12 9:57 AM, Christian Blouin wrote:
My simulation aborts rather quickly because it accumulates too many
LINCS warning. I checked the various plots and everything seems to be
stable (temperature, pressure, total energy, etc.). The stderr gives
me warnings looking like this:
Step
On 8/2/12 10:09 AM, vidhya sankar wrote:
Dear Gromacs user , I Write Some linux .sh programming to automate
grompp and mdrun process in Clustering which is as Follows
Could Any one of you point out the error in following script files ? is it
correct or not.
Are you getting
The number of lipids deleted by InflateGRO is printed to the screen. Update the
[molecules] section of your .top accordingly.
-Justin
On 8/2/12 7:32 AM, Bhavaniprasad.V wrote:
hello all,
even i am having a similar problem. after running inflategro.pl.how to find the
number of deleted
On 8/3/12 12:32 AM, Bhavaniprasad.V wrote:
hi justin,
the problem is actually InflateGro is not deleting any lipids.
I had inserted the protein in lipid using VMD and saved the coordinate file and
using that directly to this step
cat pro_in_pope.gro pope_whole.gro system.gro
after running
On 8/3/12 10:27 AM, Steven Neumann wrote:
Dear Gmx Users,
I want to simulate protein line chain (80 residues) in explicit
sovent. Let's assume its axis is x direction. What should be the z and
y dimension of the box? Is there any rule? Would you wait e.g. for 50
The box size in all
On 8/3/12 10:47 AM, Steven Neumann wrote:
On Fri, Aug 3, 2012 at 3:34 PM, Justin Lemkul jalem...@vt.edu wrote:
On 8/3/12 10:27 AM, Steven Neumann wrote:
Dear Gmx Users,
I want to simulate protein line chain (80 residues) in explicit
sovent. Let's assume its axis is x direction. What
it personally, but others do.
-Justin
Regards
Bhavaniprasad
-Original Message-
From: Justin Lemkul
Sent: 3 Aug 2012 10:54:49 GMT
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Re: number of coordinates in coordinate file
(system_inflated.gro, 9331) number
On 8/3/12 11:01 AM, bhavaniprasad vipperla wrote:
Hi
I tried to run the minimization step . Minimization went on well but am not
confout.gro
Is there any specific command for obtaining an confout.gro while running em.
If mdrun did not write an output .gro file, then it did not complete.
On 8/4/12 10:31 AM, juanjuan0618 wrote:
On 1/08/2012 11:29 PM, juanjuan0618 wrote:
Dear professor,
Now I want to simulate the water and carbon dioxide mixture solution,but
when I do the simulation with my own .gro and .itp files, I met some
questions.
I use gromacs4.0.7 and the water model
On 8/5/12 12:16 PM, juanjuan0618 wrote:
I'm sorry to disturb you again.
The previous questions have been solved. I delete the [ atomtypes ]
description in the CO2.itp file and then the error is removed.
But I have another question to ask you, can you tell me the meaning of
molname, nrexcl,
On 8/5/12 4:46 PM, Ali Alizadeh wrote:
Dear all users
In my pdb file that contain ethane or propane or other molecules,
there are LIG residue in my pdb file that gromacs could not found
them, how to add this LIG(in our pdb files) for my force field?
This residue(LIG) exists in all pdb files
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