Please start a new thread if you're going to introduce a new topic. I have
changed the subject to something more relevant.
On 4/29/13 4:23 PM, lloyd riggs wrote:
*Dear All,*
*Doing a water/temp energy minimization just for a figure with a large molecule
that has several connected parts, I ra
On 4/29/13 8:00 PM, Mark Abraham wrote:
On Mon, Apr 29, 2013 at 11:34 PM, Justin Lemkul wrote:
Please start a new thread if you're going to introduce a new topic. I
have changed the subject to something more relevant.
On 4/29/13 4:23 PM, lloyd riggs wrote:
*Dear All,*
*Doing a
ed with the improper term does not differ significantly. Minor
differences noted, but within error, hence standard MD at play :) For any other
order, things go haywire.
-Justin
On Tue, Apr 30, 2013 at 2:06 AM, Justin Lemkul wrote:
On 4/29/13 8:00 PM, Mark Abraham wrote:
On Mon,
On 4/29/13 9:30 PM, maggin wrote:
Hi,
when I use GROMACS4.5.5 to do peptid simulation. At NVT step, system is not
equilibration, so I extend NVT simulation as follows:
tpbconv -s nvt.tpr -extend 2000 -o next1.tpr
mpirun -np 4 mdrun_mpi -reprod -s next1.tpr -cpi nvt.cpt
after finish this e
On 4/30/13 2:59 AM, Nikunj Maheshwari wrote:
Dear all,
I got an error while using pdb2gmx command (pdb2gmx -f 123.pdb -o
output.gro)
I used 13. GROMOS 53a6 force field
"Fatal error:
Atom HA in residue GLU 1 was not found in rtp entry GLU with 12 atoms while
sorting atoms.
For a hydrogen, th
If you are starting a new topic, please give it an informative subject line and
do not reply to a digest message.
On 4/30/13 3:37 AM, Arunima Shilpi wrote:
hello sir
there was error in running grompp file of umbrella sampling... the error it
says
"no such molecule type sol" found...
ho
o there is a
conflict. HISD and HISH work because they both should have a proton on ND1.
-Justin
On Tue, Apr 30, 2013 at 3:33 PM, Justin Lemkul wrote:
On 4/30/13 2:59 AM, Nikunj Maheshwari wrote:
Dear all,
I got an error while using pdb2gmx command (pdb2gmx -f 123.pdb -o
output.gro)
On 4/30/13 10:58 AM, James Starlight wrote:
Dear Gromacs users!
I have a question about umbrella sampling simulation based on the Justin's
tutorial.
According to the tutorial after definition of the set of conformers
extracted from the pulled trajectory I should run N equilibrating
simulatio
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 4/30/13 12:33 PM, lloyd riggs wrote:
I appologise, I meant defined at the same time without complaining, not just
either direction.
A different atom order is interpreted as a different interaction. In this case,
if both are defined, there is indeed a difference in the improper energy ter
On 4/30/13 1:38 PM, James Starlight wrote:
Justin,
could you also tell me
1) what difference should be expected from the umbrella sampling run with
(as I want to do for better coverage) and without (as in your tutorial)
velocities re-assignment on each umbrella window run ?
You have to dis
On 4/30/13 3:03 PM, Sikandar Mashayak wrote:
Hi
I am following the git tutorial for the novice. It says to check out stable
version
one should use "git checkout --track -b release-4-5-patches
origin/release-4-5-patches"
Is there stable branch for 4.6? If yes, how do get it? I tried replacing
On 4/30/13 4:19 PM, Reza Salari wrote:
Hi
I have set up two small systems, one with a single POPC lipid, and another
system with 23 POPC's arranged as a lipid bilayer. I am hoping to do a
similar comparison as in Table 1 in the Par Bjelkmar et al paper (porting
charmm ff to gromacs) for my sys
On 4/30/13 8:01 PM, Sikandar Mashayak wrote:
Hi
I found the branch of gromacs code called localpressure-4.0 at
http://redmine.gromacs.org/projects/gromacs/repository/show?rev=localpressure-4-0.
I am wondering whether this code can compute the spatial variation of
pressure in given system. And
On 4/30/13 8:28 PM, Sikandar Mashayak wrote:
Thanks Justin.
I replaced release-4-5-patches with release-4-6 while checking out the
branch.
When I installed it and checked the version string I get VERSION
4.6.2-dev-20130429-d13fc48.
Does that mean I got the version which is still under developm
On 4/30/13 8:50 PM, Sikandar Mashayak wrote:
Hi Justin
Thanks for explanation. But I am a bit confused because I am new to git.
When I check out release-4-6 branch, the source code should be the same as
the one in tarball from Gromacs website, right? When I run git status I get
# On branch rel
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
On 5/1/13 12:58 AM, Arunima Shilpi wrote:
hi alll
How to generate input.pdb file for umbrella sampling.
As I told you yesterday
(http://lists.gromacs.org/pipermail/gmx-users/2013-April/080834.html), please
don't reply to a digest, and if you're starting a new thread, give it an
ature request on redmine.gromacs.org - it's the only official
way we keep track of fixes and features. If it's not there, it likely won't get
addressed until one of the developers has a compelling need to work on it.
-Justin
On May 1, 2013, at 2:34 AM, Justin Lemkul wrote:
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
On 5/1/13 8:40 AM, George Patargias wrote:
Hello
I am trying to calculate the MSD of 8 molecules in a lipid bilayer with
g_msd. If I include the atoms of all these 8 molecules as a single group
in the index file, will g_msd calculate the MSD of the center of mass of
them or it will average ove
On 5/1/13 7:50 PM, bharat gupta wrote:
Dear gmx-users,
I got the following error after issuing the final command for running 12
replicas :-
[bme:42039] *** Process received signal ***
[bme:42039] Signal: Segmentation fault (11)
[bme:42039] Signal code: Invalid permissions (2)
[bme:42039] Fail
On 5/2/13 1:54 AM, bipin singh wrote:
Hi All,
I want to calculate temperature for each individual amino acids residues
present in a protein after the simulation. I know that this can be done
with help of g_traj, but my concern is whether this will give me correct
temperature or not because it
On 5/2/13 12:38 AM, Mohan maruthi sena wrote:
Hi all,
I have system consisting of a peptide(alpha-helix), I want the
peptide to be surrounded by magnesium ions(instead of water). How can i do
this gromacs? How can I find the concentration of magnesium ions. just like
in solution we
On 5/2/13 7:33 AM, Mohan maruthi sena wrote:
Hi ,
Thanks for a quick reply. Sorry for not being clear, I want to
surround the peptide with just ions(sodium). How can I do this?
genbox -ci -nmol
You will need a coordinate file for a single Mg2+ ion to be inserted, which is
trivia
On 5/2/13 8:40 AM, Souilem Safa wrote:
Dear Gromacs users ,
I did the simulation of a single molecule in vacum. I have choosed 10 ns
which corresponds to 500 steps. I was checking the .log file frequently.
I have noticed that the number of steps from 1938900 didn't increases.
When I open
On 5/2/13 8:57 AM, Souilem Safa wrote:
Thank you for your quick answer
I have joined here my mdp file and the toplogy one also.
The mailing list does not accept attachments. Please copy and paste the text
into an email. We may not need the whole topology, but a description of what
you're
x27;s
value by a constant and then averaging gives the same as averaging and
multiplying by a constant.
-Justin
On Thu, May 2, 2013 at 4:56 PM, Justin Lemkul wrote:
On 5/2/13 1:54 AM, bipin singh wrote:
Hi All,
I want to calculate temperature for each individual amino acids residues
pres
.
Use of the scaling factor depends on what you want to observe, but multiplying
each frame's value by a constant and then averaging gives the same as averaging
and multiplying by a constant, so you might save yourself some work if you just
care about averages.
-Justin
On Thu, May 2, 20
On 5/2/13 11:01 AM, Dubi wrote:
Dear Gromacs Community,
I m in the situation where I have a trajectory that started in a geometric
position "A" and ended in position "B". If I hit a new mdrun with the
"-append" extension, than the trr output is the old trajectory together with
the new one whic
On 5/2/13 2:16 PM, Jesper Sørensen wrote:
The shape is a sphere not a circle, what the picture is showing is a cut
through the vesicle. Have you googled lipid vesicles?
I don't know of a place that will have template systems like this for you. But
you should be able to get these by making a l
On 5/3/13 5:39 AM, Souilem Safa wrote:
Dear Gromacs users,
I m aiming to install gromacs 4.5.5 package in in linux Fedora 18. I have
updated the needed compilers and downloaded the fftw-3.3.2.tar.gz and
gromacs4.5.5.tar.gz
I have followed these commands to install:
$ tar -zxvf fftw-3.3.2/
$ cd
On 5/3/13 5:41 AM, Monoj Mon Kalita wrote:
Dear Users
Can Anybody help me to simulate a water box with nearly 14.45 A box size
and approximately 93 water molecules. I have tried to simulate it using the
'spc' water model. I have done the SD and CG minimization step. Till that
step it was fine
On 5/3/13 12:10 AM, Arunima Shilpi wrote:
Hello sir
I got the following error while running pulling
mdrun -s pull.tpr
"distance of pull group 1 is larger than the box size"
I request you to kindly guide me in overcoming the error
Since we know nothing of what you are doing or how you ar
On 5/3/13 11:27 AM, Ewaru wrote:
Hi,
Just wondering. My system shows this: "System has non-zero total charge:
11.98"
and thus, I use the command as below to add 12 Cl to the protein:
"genion -s ions.tpr -o m4_solv_ions.gro -p topol.top -pname NA -nname CL -nn
12"
However, when I checked
LJ -995.0311 -1219.3432 -224.3121
Pot 3084.9904 2993.2110 -91.7794
Something you think is equivalent is not :-) Move to testing a system with
two lipids. Inspect all the logfile outputs very carefully for clues.
Mark
On Tue, Apr 30, 2013 at 8:33 PM, Justin Lemkul wrote:
On 4/30/13 4
On 5/3/13 7:56 AM, Ahmet yıldırım wrote:
Dear users,
I tried to calculate the order parameter of benzene ring of the ligand
using g_order but I have a error as the following :
make_ndx -f topol.tpr -o order.xvg
a C1 C2 C3 C4 C5 C6
Found 6 atoms with names C1 C2 C3 C4 C5 C6
26 C1_C2_C3_C4_C5_
On 5/3/13 11:52 AM, Ewaru wrote:
Hi Justin,
Thank you for your prompt reply! My grompp goes like this: "grompp -f
minim.mdp -c m4_solv_ions.gro -p topol.top -o em.tpr"
Is it in the topol.top file? The reason I'm asking this is because I
obtained this error while running MD:
Yes, you should
On 5/3/13 2:21 PM, James Starlight wrote:
Couple extra question about umbrella
Does it possible to use Collective variable (eigenvector from EDA or NMA)
as the pulling coordinate?
Does it possible to use output from essential dynamics sampling (here I can
use EDS in targeted mode to pull my st
On 5/4/13 8:28 PM, Amir Abbasi wrote:
Hi All,
I want to simulate graphene oxide in water. i have used swissparam server to
create .itp file of it.
then i'd put the .itp file in oplsaa.ff folder and edit forcefield.itp file and
insert:
#include "GRO.itp"
Do not edit forcefield.itp in this wa
itp to top?
Sure. They're hardly different.
http://www.gromacs.org/Documentation/File_Formats/Topology_File
Depending on what the contents of your system are, you may be almost 90% done
with the topology you will need.
-Justin
or there is an other way?
____
On 5/4/13 8:44 PM, Amir Abbasi wrote:
Hi,
I have epoxide group in the molecule that i want to simulate. but there is no
parameters reported for this functional group.
How can i obtain parameters of epoxide group?
Derive them in a manner consistent with the parent force field that you have
On 5/5/13 5:10 AM, Group Gro wrote:
Dear GROMACS users,
I am working on protein-ligand complexes and when I run "mdrun -deffnm nvt.tpr
-v" I run into this error:
Fatal error:
2 particles communicated to PME node 1 are more than 2/3 times the cut-off out
of the domain decomposition cell of th
On 5/5/13 12:40 PM, Shima Arasteh wrote:
Hi,
I' like to know if it is possible to get the average RMSD through g_rms
command? Or I need to get it manually?
Use g_analyze.
-Justin
--
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochem
On 5/6/13 4:21 AM, gromacs query wrote:
Dear All,
I want to calculate water and ions density around polymer. After MD I see
my polymer goes near the edges of box and rather some part is out of box.
So in order to calculate water and ion density I think polymer should be
near the center of box
On 5/6/13 6:51 AM, Sathish Kumar wrote:
hai
i would like to use Reax force field,can we use reax force field
in gromacs and if any one please tell to me weather reax ff is useful for
protein
It won't be easy to use Reax, if it's even possible. You would have to make
some serious
On 5/6/13 7:03 AM, Sathish Kumar wrote:
I want to do simulation of protein at pH 12, in this case experimentally
reported that the disulphide bonds of protein was broken and sulphurs
become S negative . Can you please tell me making of disulphide as S- and
S- is it correct and how to set fo
On 5/6/13 7:32 AM, gromacs query wrote:
Dear Justin,
You don't need to change the trajectory in any way to do density
measurements
I read sometime before in some paper: water density falls around polymer
(COM) at a distance nearly 4.5nm when it is in box of 10x10x10 nm. I assume
the polymer
Please use informative subject lines. "No subject" often gets flagged as spam,
and thus people who may be able to help you may never see your message.
On 5/6/13 7:58 AM, Sathish Kumar wrote:
I want to do simulation of protein at pH 12 so i have to deprotanate
tyrosine,tryphtophan.Can you ple
On 5/6/13 2:16 PM, Bryan Roessler wrote:
Hello,
I have successfully generated a 945MB mtx hessian storing the normal modes
of a ~1500AA protein using mdrun with the "nm" integrator and no cutoffs.
However, when I try to analyze the normal modes and create trajectories
using g_nmeig, I can't se
On 5/6/13 5:58 PM, jhon michael espinosa duran wrote:
Hi all
I am doing an NVE simulation of a protein immersed in water, and I want
to keep track of the potential energy in the protein. Do you know how can I do
it?.
I tried saving the energy of the protein ( the protein as an energy group)
On 5/6/13 9:39 PM, Andrew DeYoung wrote:
Hi,
I am running mdrun-gpu on Gromacs 4.5.5 (with OpenMM). This is my first
time using a GPU. I get the following error message when attempting to run
mdrun-gpu with my .tpr file:
---
Program mdrun-
On 5/7/13 1:05 AM, Arunima Shilpi wrote:
Hello Justin sir
In your tutorial file for umbrella sampling for Aβ42 protofibril, what was
the criteria used to determine the coordinates of center of mass and box
size which you have takes as
editconf -f complex.gro -o newbox.gro -center 3.280 2.181
On 5/7/13 6:40 AM, Natalie Stephenson wrote:
Hi,
I know there have been many threads talking about parameterization of novel
molecules for simulations within gromacs, but I just wanted to know if anyone
had done any parameterization of myristic acid, as I intend to begin
simulations on a prot
On 5/7/13 1:04 PM, Sun Moon wrote:
Hi
I have been using the lipids from Prof Tieleman's website and (using Berger
Lipids) in gromacs 4.5.4 I want to try the grompp tool but have encountered
this problem:
Fatal error:
Atomtype C not found
This atomtype belongs to protein functional grou
On 5/7/13 2:04 PM, Za Pour wrote:
Dear gmx users
I would like to calculate the number of the surfactant molecules adsorbed on the
nanotube surface as a function of time. I would be pleased if anyone could tell
me
whether there is a program in gromacs to do that or not?
Not directly, but perh
uding the following:
1. Exact commands given in the preparation protocol (EM and equilibration)
2. The .mdp files being used for all steps, most importantly NPT and MD
3. Your grompp and mdrun invocations for the failing MD run
-Justin
- Original Message -
From: Justin Lemkul
To:
On 5/8/13 8:16 AM, Arunima Shilpi wrote:
Hello Sir
While running command for perl distances.pl.. system gets hanged...while
processing particular group file...
I will be thankful to you if you can guide me in debugging the error
If you created groups.txt in accordance with what the tutori
On 5/8/13 3:07 AM, Subramaniam Boopathi wrote:
Dear Sir,
I am succesfully run molecules upto energy minimization, in case of
position restrain md step , i have following, could you help to overcome
the A charge group moved too far between two domain decomposition steps.
Step 1, time 0
On 5/8/13 2:35 AM, Shima Arasteh wrote:
OK.
1. Exact commands given in the preparation protocol (EM and equilibration)
EM:
# grompp -f minim.mdp -c input.gro -p topol.top -o minim.tpr
#mdrun -deffnm minim
NVT:
#grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
#mdrun -deffnm n
On 5/8/13 9:19 AM, Sainitin Donakonda wrote:
Hello,
I am trying to secondary structure analysis using DSSP in gromacs so i
followed this procedure
First I downloaded dssp
wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64 -O
~/dssp
this gave dssp executable file in my home
On 5/8/13 11:09 AM, Gmx QA wrote:
Hi gmx-users,
I've been experimenting with simulations of mixed bilayers (512 lipids in
total, 70% POPC, 30% POPE) using the charmm36 parameter set in gromacs, and
have a couple of questions. I know this has been discussed before, but I'd
appreciate some input
On 5/8/13 12:44 PM, Gmx QA wrote:
Thanks Justin, those are good points.
A quick follow up, would you (or someone else) consider the APL-values I
have for my mixed bilayer system to be good, just ok-ish or plain wrong?
I have no basis for making such an assessment, but I know there is litera
On 5/8/13 2:55 PM, zugunder wrote:
Hi,
Hi, I have a rather odd problem running do_dssp:
$ do_dssp -h
bash: do_dssp: command not found
I am running GROMACS 4.5.7 under SL 6.3 and everything else seems to work
fine.
DSSP is also installed and should be OK:
$ dssp -h
DSSP 2.0.4 options:
-h
On 5/8/13 3:03 PM, zugunder wrote:
Sorry guys, just figured it out:
correct syntax is g_do_dssp :-)
Maybe, it would worth correcting the online manual for GROMACS (which is for
4.6.1 version now)? do_dssp and editconf are mentioned there without "g_"
prefix, unlike many other commands...
Pr
On 5/8/13 3:25 PM, zugunder wrote:
OK, thanks a lot, got it.
But suddenly I got an unexpected error executing do_dssp:
Program g_do_dssp, VERSION 4.5.7
Source code file: /builddir/build/BUILD/gromacs-4.5.7/src/tools/do_dssp.c,
line: 572
Fatal error:
Failed to execute command: /usr/local/bin/
On 5/8/13 4:20 PM, zugunder wrote:
And it seems to me more strange as there is no option "-na" - neither in
dssp, nor in do_dssp.
Or do I missing something? Just in case, here is my command:
$ g_do_dssp -s md_input_extended_to50ns.tpr -f md_product.xtc
where:
.tpr - after I extended the pro
On 5/8/13 5:33 PM, zugunder wrote:
Thank you Justin, but I am afraid I do not understand what you mean.
I am using gromacs 4.5.7 and there are no traces of -var option in its
manual (actually, for 4.5.6); moreover, if I try to specify -ver in the
command I get an error on an invalid command li
On 5/8/13 6:24 PM, zugunder wrote:
OK, thank you, now it is clear.
So, that's what I've done so far:
1. Got a dsspold binary for Linux (unfortunately, 32bit only).
2. Renamed it into dssp, moved to /usr/local/bin and made it executable with
chmod a+x
3. Because of dsspold being 32bit (giving
On 5/8/13 6:59 PM, zugunder wrote:
But don't you know where I could find the default settings used in xpm to eps
conversion (without di flag)?
The default values simply indicate that each element occupies 1 pixel, such that
you have some matrix that is N residues by some tens of thousands (m
On 5/8/13 7:18 PM, zugunder wrote:
May I ask you to share the content of your m2p?
The size of the matrix elements is subjective; it depends on what dimensions of
the matrix you want. My usual settings are xbox = 0.05, ybox = 2.0, but that's
for my systems, which are relatively small alon
On 5/9/13 9:35 AM, Anirban wrote:
Dear ALL,
I want to randomize the frames of my trajectory for calculating
convergence. For this, I have dropped the frames as PDB files using trjconv
and then renamed them randomly. Now I want to join these randomized PDB
frames to get a randomized trajectory
On 5/9/13 9:50 AM, Anirban wrote:
Thanks a lot Justin, for the reply.
But with -settime for every file I have to interactively give arbitrary values.
I have around 500 PDB files for one part of the trajectory and there are total
10 parts. So its very difficult to repeat this for around 5000 ti
On 5/9/13 10:15 AM, mohammad agha wrote:
Dear GROMACS Specialist,
I want to plot probability (nm^-1) distribution of micelle selected atoms with
respect to COM of the micelle (nm).
with respect to this definition, "Probability was defined as the number of instances
the selected atom was fo
On 5/9/13 4:33 PM, Eric Stokes wrote:
Hello,
I am attempting to generate force-field parameters for a fatty acid
molecule that contains a carboxilic acid head group. I decided to use the
parameters for stearic acid as the base for my molecule, since they contain
similar structures with the onl
On 5/10/13 12:35 AM, Arunima Shilpi wrote:
Hello sir
As in the tutorial for umbrella sampling command
make_ndx -f npt.gro
you have selected two different groups as Chain_A as 19 and Chain_B as 20
If we have protein-ligand interaction whether we should have single group
of protein-ligand comp
On 5/10/13 1:55 AM, Shima Arasteh wrote:
Hi,
In Umbrella Sampling method, among mdp settings, there is a section where the
pull code settings are defined in:
pull = umbrella: using a harmonic potential to pull
As it is said that "with US the path of the permeating ion along thereaction
coo
On 5/10/13 4:24 AM, Nawel Mele wrote:
Hi,
I am trying to understand what is the difference between g_rms and
g_rmsdist commands.
I have looked at the manual and all I can find is that:
*g_rms*: The root mean square deviation (RM SD) of certain atoms in a
molecule with respect to a reference
s
On 5/10/13 5:16 AM, Jernej Zidar wrote:
Hi,
In CHARMM I generated a short peptide. The N-terminal is a regular
-NH2 (patch NNEU) while the C-terminal is amidated (patch CT2).
I would like to import the PDB to GROMACS using pdb2gmx by using the
CHARMM27 forcefield later. I issue the foll
On 5/10/13 11:27 AM, mohammad agha wrote:
Dear GROMACS Specialists,
I have one problem with g_dist. When I use g_dist along with option -dist, the
output is printed on the terminal, but I want them into a file as separately.
May I ask you to help me, Please?
Redirect the terminal output int
On 5/10/13 11:46 AM, mohammad agha wrote:
Dear Justin,
Thank you very much from your answer.
May I ask you to help me more, Please?
I work with UBUNTU, I don't know how should I do it!
Apply Google. This is not a Gromacs issue and should be investigated and
studied in the appropriate for
On 5/11/13 12:38 AM, Arunima Shilpi wrote:
Respected Sir
Presently my work includes umbrella sampling for protein ligand
interaction. The components of md_pull.mdp is
title = Umbrella pulling simulation
define = -DPOSRES_B
; Run parameters
integrator = md
dt = 0.002
tinit
decomposition cell of their charge group in
dimension x.
This usually means that your system is not well equilibrated.
Would you please give me your suggestions?
Sincerely,
Shima
- Original Message -
From: Shima Arasteh
To: Justin Lemkul ; "gmx-users@gromacs.org"
Cc:
Se
On 5/11/13 5:37 AM, Sun Moon wrote:
Hi,
I am doing pure membrane simulation in DOPC environment (using Berger
Lipids) in Gromacs 4.0.7 I want to try the grompp tool but have
encountered this problem:
Fatal error:
Atomtype OW not found
Topology file is as
the following:
#include "lipid.itp"
On 5/11/13 9:56 AM, Christopher Neale wrote:
Perhaps it is just the way I am doing things then. From my viewing, there were
4 posts yesterday that required me to scroll horizontally when reading in my
browser (This line too will come out requiring scrolling on the gmx list page
that I find m
On 5/12/13 2:25 AM, Hyunjin Kim wrote:
Dear,
I want to calculate LJ and Electrostatic energies between two groups
defined in index.ndx during rerun with original trajectory.
The following is what I tried:
1. insert "energygrps r_1 r_25" in the test.mdp file.
2. grompp -f test.mdp -c x.gro -
On 5/12/13 6:40 AM, Arunima Shilpi wrote:
Respected Sir
many many thanks for your reply to my last mail. while running
trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep
I selected group 0 for the system...
but while i run perl distances.pl
it says processing file 236...and than the system
On 5/12/13 8:48 AM, mohammad agha wrote:
Dear GROMACS Specialists,
I want to obtain number of instances the different atoms was found within a
spherical shell of width 0.02 nm at a distance r
from the micelle COM. For this, I use g_dist -dist, but when I select for
example 0.04, it also resu
On 5/12/13 12:54 PM, Hyunjin Kim wrote:
On 5/12/13 2:25 AM, Hyunjin Kim wrote:
Dear,
I want to calculate LJ and Electrostatic energies between two groups
defined in index.ndx during rerun with original trajectory.
The following is what I tried:
1. insert "energygrps r_1 r_25" in the test.
On 5/12/13 1:14 PM, Hyunjin Kim wrote:
On 5/12/13 12:54 PM, Hyunjin Kim wrote:
On 5/12/13 2:25 AM, Hyunjin Kim wrote:
Dear,
I want to calculate LJ and Electrostatic energies between two groups
defined in index.ndx during rerun with original trajectory.
The following is what I tried:
1.
On 5/12/13 1:17 PM, tarak karmakar wrote:
Dear All,
I am simulating a protein in water to check the ligand movement over a
time span. I haveminimized the system in STEEP and CG and after that
heated from 0K - 300K within a time span of 300 ps. Then, I performed the
NPT production run
On 5/12/13 1:34 PM, tarak karmakar wrote:
Thanks Justin for the Quick and Helpful reply.
Yes. If I am right, the chaotic behavior of the simulations is inherent
and can be assessed statistically by generating several independent
trajectories and analyzing their similar outcomes. But with t
On 5/12/13 1:31 PM, Hyunjin Kim wrote:
On 5/12/13 1:14 PM, Hyunjin Kim wrote:
On 5/12/13 12:54 PM, Hyunjin Kim wrote:
On 5/12/13 2:25 AM, Hyunjin Kim wrote:
Dear,
I want to calculate LJ and Electrostatic energies between two groups
defined in index.ndx during rerun with original traje
lincs_warnangle = 30
On Sun, May 12, 2013 at 11:11 PM, Justin Lemkul wrote:
On 5/12/13 1:34 PM, tarak karmakar wrote:
Thanks Justin for the Quick and Helpful reply.
Yes. If I am right, the chaotic behavior of the simulations is
inherent
and can be assessed statistically by generating
On 5/12/13 1:53 PM, Hyunjin Kim wrote:
On 5/12/13 1:31 PM, Hyunjin Kim wrote:
On 5/12/13 1:14 PM, Hyunjin Kim wrote:
On 5/12/13 12:54 PM, Hyunjin Kim wrote:
On 5/12/13 2:25 AM, Hyunjin Kim wrote:
Dear,
I want to calculate LJ and Electrostatic energies between two
groups
defined in
On 5/13/13 1:48 AM, Acoot Brett wrote:
Dear All,
Will you please explain how the initial velocity may affect the MD results?
We use different initial velocities to improve sampling, i.e. to allow the
trajectory to evolve in different ways. In the end, in the limit of infinite
sampling, th
On 5/13/13 4:44 AM, Sainitin Donakonda wrote:
Thank you very much for inputs but i forgot to mention in previous query i
got one error ..with other protein ligand simulation i used same MD file
saving 200 steps..
*Cannot write trajectory frame; maybe you are out of quota?*
*
*
Whats the soluti
On 5/13/13 5:33 AM, Arunima Shilpi wrote:
Respected Sir
many many thanks for your reply to my last mail. I was able able to debug
the error
Here I have new set of queries..
How much COM spacing should i consider for my protein-ligand interactiom
How much total distance I should move along z-a
On 5/13/13 6:10 AM, Nawel Mele wrote:
Hi all,
I am performing a simulation of protein at air/water interface.
For create an air-water interface I just expand the box in the z direction.
So,aAfter minimization we can noticed that water molecules moved out of
bulk water in the z direction.
Why
On 5/13/13 6:30 AM, Laura Leay wrote:
All, I have a system of nitric acid modelled as NO3- and HO3+ plus SPC water.
After setting the system up using genbox I then energy minimise. Althouth the
input conf.gro file looks fine (NO3- labelled 'NO3', HO3+ labelled 'HO3' and
water labelled 'SOL')
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