On 8/19/14, 8:46 AM, Atila Petrosian wrote:
Dear gromacs users
I would like to compute the radial density profile (1/nm-3) of
different parts of a micelle formed with SDS molecules (such as headgroup,
alkyl tail and water) relative to the center of mass of the micelle.
Is there a direct
On 8/19/14, 9:02 AM, Atila Petrosian wrote:
Dear Justin
Thanks for your quick answer.
I want to obtain *radial density profile* relative to COM and not radial
distribution function (RDF) relative to COM.
Are you sure g_rdf -com is appropriate for this aim?
Sorry, misread. gmx density
On 8/19/14, 9:08 AM, Dawid das wrote:
Dear Gromacs experts,
How can I understand the relation between those four last columns:
@ s0 legend Rg
@ s1 legend RgX
@ s2 legend RgY
@ s3 legend RgZ
0 1.6378 1.2375 1.37115 1.39762
2 1.6433 1.25186
On 8/19/14, 10:30 AM, Ali Alizadeh wrote:
Dear All users,
I have been engaged in answering this questionhow long should we continue
calculating to make sure we can get justifiable results?. Are there any
suggestions to dig out to find out when a system converges? I know this is
a too general
On 8/19/14, 11:03 AM, Nikolaos Michelarakis wrote:
Hello,
I am trying to measure the distances between certain residues over the
course of my simulation. I have created an index with these residues. So
far i have tried using gmx mdmat but since there are only five residues the
resulting map
On 8/19/14, 12:45 PM, Dawid das wrote:
Dear Gromacs experts,
In my MD simulation I noticed that protein drifts toward one of the faces
of cubic solvation box. Now I use periodic boundary conditions but one of
the residues sticks out of solvation box. My general question is: is it
okay or
On 8/19/14, 2:14 PM, pragna lakshmi wrote:
Dear all,
I am trying to do MD simulation of POPC membrane simulation with peripheral
attachment of protein ligand complex. Steps that i have performed so far
are:
1. orienting the protein with editcong -princ command
2. rotating it along the y-axis
On 8/19/14, 1:16 PM, Dawid das wrote:
I was trying to calculate total dipole moment for one residue of protein
and I got this error:
Fatal error:
index[1]=972 does not correspond to the first atom of a molecule
Is it possible at all to calculate dipole for one residue inside aminoacid
On 8/19/14, 8:29 PM, Smith, Micholas D. wrote:
Hi gmx_users,
I am trying to run a simulation that includes a sucrose molecule constructed
with the CHARMM36 AGLC and BFRU carbohydrate residues. The problem is when I
run pbd2gmx with the system, the sucrose molecule splits into a separate
On 8/19/14, 9:03 PM, Smith, Micholas D. wrote:
So the topology file that is written for the sucrose molecule is: [
moleculetype ]
; Namenrexcl
Other 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
;
: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul
jalem...@vt.edu
Sent: Tuesday, August 19, 2014 9:10 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] CHARMM36 sucrose?
On 8/19/14, 9:03 PM, Smith, Micholas D. wrote:
So
On 8/20/14, 12:56 PM, pragna lakshmi wrote:
Thank you Mark for ur reply.
In the generated POPC.top from POPC.pdb and POPC.psf using VMD, the charges
have become to zero. Here are few lines of my POPC.top
[ atomtypes ]
; name bond_type mass charge ptype sigma epsilon
C1 C 1.0 0.0 A 0.0 0.0
C11
On 8/20/14, 12:02 PM, Dawid das wrote:
I found one problem. If I create new group in index.ndx file which contains
protein without CH6 residue then some h-bonds are detected but actually I
wouldn't expect it the way it looks.
So again, how does actually g_hbond calculate hydrogen bonds except
On 8/20/14, 3:59 AM, Meenakshi Rajput wrote:
hello users
I had done energy minimisation of protein-ligand complex and i got negative
potential. Also the ligand was at right place after EM run but when I tried
the positional restrained run, too many lincs warnings came and md run
stopped
On 8/20/14, 5:27 AM, Albert wrote:
Hello:
I am just wondering is it possible to delet water molecules within 4A of a
ligand through Gromacs command line? Everytime I have to do this in VMD which
is a little bit complecated.
g_select can do this. It can give you an index group of
On 8/20/14, 6:33 AM, Dawid das wrote:
Dear Gromacs experts,
I googled for answer and I found these:
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
http://www.researchgate.net/post/How_to_extend_the_protein_simulation_in_Gromacs_from_1000_ps_to_1_ps
but still I am
On 8/20/14, 8:54 PM, MUSYOKA THOMMAS wrote:
Dear Users,
I am working on protein-ligand MD simulation. I have managed to get the
number of H-bonds formed between the protein and ligand throughout my
simulation period. I noticed three important residue participate in the
formation of this
On 8/21/14, 5:24 AM, ankit agrawal wrote:
hi,
I was simulating A cadherin molecule (PDB ID: 4APX). I removed all the
water molecule from molecule then ran the following command.
pdb2gmx -f 4APX.pdb -water tip3p
then I chose force field : CHARMM27 (with CMAP) after that it should create
3
On 8/21/14, 3:11 PM, Agnivo Gosai wrote:
Dear Users
I initially installed GROMACS 5.0 in my office computer and tried running a
few sample tutorials over there.
It was showing a illegal instruction : core dumped error. On searching
the archived files in the user group I found that the
On 8/21/14, 4:22 PM, ibrahim khalil wrote:
dear gromacs users, I am simulating Carbon nanotubes in water. I did the
NPT simulation with a reference pressure of 1 bar.
When I do an NPT simulation for about 100 ps, the system shows an average
pressure of 1.4 bar. So i thought a longer NPT
On 8/22/14, 8:49 AM, Dawid das wrote:
Can you just have a quick look at this?
When I run:
tpbconv -s npt-md.tpr -extend 95000 -o npt-md.tpr
to extend simulation by 95 ns this time I got this message at the end:
Extending remaining runtime of by 95000 ps (now 5000 steps)
Writing
On 8/22/14, 4:36 PM, Xiang Ning wrote:
Hi All,
I am using POPC/POPG mixed membrane built by Charmm-gui. After remove ions and
water from CHARMMGUI pdb and save just the membrane pdb, and use this pdb with
pdb2gmx to get top file (I used charmm36), then I would like to know, how to
add
On 8/24/14, 5:10 AM, Atila Petrosian wrote:
Dear gromacs users
I want to use a new code (g_vesicle_density) in gromacs being in this
address: http://md.chem.rug.nl/~mara/softa/.
There are 2 related files (g_vesicle_density.c and gmx_vesicle_density.c).
I did following steps to use this
On 8/24/14, 5:28 AM, Lovika Moudgil wrote:
Hi everyone ,
Need some help .I have got an error in my mdrun . Upto grompp every thing
was fine but when I give command for mdrun ,It stops with this ...
Steepest Descents:
Tolerance (Fmax) = 1.0e+03
Number of steps=1
On 8/24/14, 8:14 AM, shahab shariati wrote:
Hi
Before, one could search in gromacs mailing list by subject. But, now,
there is not this possibility. Why?
Because Google does the job without the overhead on the Gromacs site:
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
Conditions
On Friday, August 22, 2014 4:48 PM, Justin Lemkul jalem...@vt.edu wrote:
On 8/22/14, 4:36 PM, Xiang Ning wrote:
Hi All,
I am using POPC/POPG mixed membrane built by Charmm-gui. After remove ions
and water from CHARMMGUI pdb and save just the membrane pdb, and use this
pdb
On 8/25/14, 3:35 AM, Timothy Click wrote:
I am simulating a system in N,N-dimethylacetamide (DMA) and ions (Li+ and
Cl-) using CHARMM36. However, I have found that the ions tend to cluster
together because of the lower dielectric constant of DMA.If I lower the
formal charges (+/-0.5), the
On 8/25/14, 1:31 AM, RINU KHATTRI wrote:
use -missing in last of command pdb2gmx
This is extremely dangerous and in should not be done in the case of missing
residues as it will lead to a broken and useless topology.
-Justin
On Mon, Aug 25, 2014 at 10:54 AM, neha bharti
On 8/25/14, 10:08 AM, Ahmet yıldırım wrote:
Dear users,
I want to analysis the change of a helix in secondary structure during
simulation time but I get the following error. Why am I getting this error?
do_dssp -f traj.xtc -s topol.tpr -o ss-helix4.xpm -sc ss-helix4.xvg -n
helix4.ndx
Select
On 8/25/14, 10:10 AM, Mahboobeh Eslami wrote:
dear justin
Thank you for your guidance.
I've done it. When I use the g_sas command, and asked me the following question:
Select a group for calculation of surface and a group for output
I do not know what groups should be selected.
Read the help
On 8/25/14, 2:09 PM, Ahmet Yıldırım wrote:
I am using Gromacs 4.5.5 and old dssp (not dssp 2.x). Dssp is exist in
usr/local/bin/dssp. It is executable.
I dont have any error when I used the following command:
do_dssp -f traj.xtc -s topol.tpr
Select a group: 1 (protein)
But I get the error
On 8/25/14, 9:55 PM, Timothy Click wrote:
Thanks for the reply, Justin. I see that the third column is set to 1. Can we
add additional terms and set the third column to 2, for instance, if we add a
second term? For instance, I may want to keep the original definition from
CHARMM for the
On 8/26/14, 12:15 AM, #SUKRITI GUPTA# wrote:
Dear Gromacs users,
I want to simulate a system with graphene sheet with water around it
containing some metal ions. I want these metal ions to be present very close
to the graphene sheet. By using genbox or genion commands I can get ions to
be
On 8/26/14, 4:50 AM, yashita thakur wrote:
Thank you Justin for you help.
But I am asking about Peter C. Lai POPC lipid which is for charmm36 force
field please see the link below
http://cesium.hyperfine.info/~peter/gromacs/popc36/
Not Peter Tieleman as mention in your tutorial as it is
On 8/26/14, 10:59 AM, Xiang Ning wrote:
Dear Justin,
Thanks a lot! I am looking forward to the new version CHARMM-GUI. However, at
this moment, I was trying to put a protein inside the membrane. I used editconf
-f protein.pdb -o conf.pdb -box (my box demension x y z) and then genbox -cp
On 8/26/14, 9:29 AM, Johnny Lu wrote:
I don't have much idea about the correct numbers to set. Mostly, I copy the
old lysozyme tutorial (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme_old/03_solvate.html),
deleted the temperature and pressure couplings, and
On 8/26/14, 1:50 PM, Dawid das wrote:
Dear Gromacs experts,
Let's say that I use such an option in pdb2gmx:
-water tip3p
Then, while generating solvation box with genbox I use:
-cs spc216.gro
So my question is, what model do I actually use? SPC or TIP3P?
Whatever is in the topology.
On 8/26/14, 12:30 PM, Eric Smoll wrote:
Hello GROMACS users,
I have created an infinite liquid film system by building a slab of
molecules in a 3D periodic unit cell where two dimensions of the film (x
and y) extend out to the edge of the unit cell and one (z) does not.
I found the slab
On 8/27/14, 1:10 AM, Lovika Moudgil wrote:
Hi everyone ,
I have a question , If coordinates of my .pdb file and .top file are not
matching than what is the right way to correct it ! Like if I have one
coordinate more in .pdb than in .top and I delete one from .pdb ...and it
get fine !!! Will
On 8/27/14, 6:24 AM, Negar Parvizi wrote:
Dear Gromacs users I have submitted a simulation for 10 ns. Now when I
started to plot the graphs such as RMSD, I saw that it has stopped at 8 ns.
The point is that although the run has stopped before specified time, I see
in md.log file the time
a simulation of united-atom phenol, I
could use -missing when processing a coordinate file containing a residue name
TYR but without the backbone atoms.
-Justin
On Mon, Aug 25, 2014 at 6:38 PM, Justin Lemkul jalem...@vt.edu wrote:
On 8/25/14, 1:31 AM, RINU KHATTRI wrote:
use -missing in last
On 8/27/14, 7:54 AM, neha bharti wrote:
I am trying to perform MD for protein ligand complex in popc lipid with
charmm36 force field and also follow Justin A. Lemkul tutorial.
I have created protein ligand complex as mention in Justin A. Lemkul
Protein-Ligand Complex tutorial till Build the
On 8/27/14, 10:14 AM, Xiang Ning wrote:
Hi all,
I was trying to put a protein inside the membrane (generated by Charmm-Gui and I made some modification). I used editconf
-f protein.gro -o conf.gro -box (my box demension x y z) and then genbox -cp conf.gro -cs lipid_water_ion.gro -o
box.gro
On 8/27/14, 11:41 AM, Xiang Ning wrote:
Dear Justin,
Sorry I missed the reply for yesterday. So the atoms are mostly from my peptide:
319: atom C of VAL, 321: N of ILE, 323: CA of ILE, 338, C of ILE, and one from
lipid POPC: 341: atom N of POPC. I just used pdb2gmx -f box.gro -p box.top to
On 8/27/14, 2:01 PM, Eric Smoll wrote:
Hello Gromacs Users,
Is there a way to output the distance between and atom X and all atoms
within distance R of atom X along a trajectory?
I am paging through the manual but I can't seem to find anything like this.
I would settle for the coordinates
On 8/27/14, 2:10 PM, ms wrote:
Dear Gromacs users,
I am using Gromacs 4.6. I would like to plot the contacts (minimum atom-atom
distances) between some residue side chains and a ligand along a trajectory. I
thought I would find the solution in g_dist or g_mindist, however, if I
understand
On 8/28/14, 2:04 PM, Dan Sponseller wrote:
Hello everyone.
I am still fairly new to gromcs but I have researched this well.
I am getting a positive potential energy (my bond energy is always positive) no
matter how long I run my simulation. I also get this when doing minimizations.
Even
On 8/29/14, 2:08 PM, Mana Ib wrote:
Dear Users,
I am doing an umbrella sampling for a protein-ligand complex, wherein I
first did an SMD run for 500 ps and generated 500 configurations, the COM
distances for these configurations start at 1.25nm for conf0 and so on till
6.4nm for conf500.
On 8/30/14, 7:17 AM, Negar Parvizi wrote:
Dear Gromacs users
I have submitted a simulation for 10 ns. Now when I started to plot the graphs
such as RMSD, I saw that it has stopped at 8 ns. The point is that although the
run has stopped before specified time, I see in md.log file the time
On 8/30/14, 8:09 AM, Mana Ib wrote:
Thankyou for your response. I spaced them at approx 0.05nm because at the
473rd configuration my ligand becomes solvated...and completely dissociated
from the protein and there is a jump in the COM distances. Would you
recommend running windows for
On 8/31/14, 6:51 AM, Dawid das wrote:
Dear Gromacs experts,
Is there a tool in Gromacs which allows one to calculate mean length,RMSD,
the minimum and maximum length of a specific bond? If yes, is it possible
to calculate it only for a specific time period of MD simulation, e.g. 3-5
ns?
On 8/31/14, 6:59 AM, Yorquant Wang wrote:
Hi all,
I want to do a membrane protein simulation and I want to use amber FF
for protein (my target protein contains many beta sheet secondary
structures). But forcefield.ff file in the web:
On 8/31/14, 8:20 AM, rajat desikan wrote:
Hi,
Slipids are already compatible with Amber. Just download the proper
lipid.itp file (DPPC.itp, DMPC.itp, ...) from the Slipids website, and
include the below line in your .top after processing your protein with
pdb2gmx (and selecting some Amber
On 8/31/14, 8:42 AM, Yorquant Wang wrote:
Hi,
I have done that according to your advice and when I do the command
grompp, I get such a error:
Fatal error:
Atomtype NTL not found
-
this is my top file:
#include amber99sb-ildn.ff/forcefield.itp
#include POPC.itp
On 8/31/14, 11:27 AM, Dawid das wrote:
Dear Gromacs experts,
I am wondering what I actually see when I plot output from g_rama. When I
run it like this:
g_rama -f 3ldj-npt-md.trr -s npt-md.tpr -o 3ldj-npt-rama.xvg
I plot the output using:
xmgrace 3ldj-npt-rama.xvg
Now I see Ramachandran
On 8/31/14, 1:17 PM, Alex s wrote:
Hi
I'd really appreciate some advice on this issue, I tend to get a segmentation
fault during my mdrun. I've searched online for ways to resolve this and tried
to diagnose whats causing this problem but I'm having no luck.
I know that if you get a
On 8/31/14, 1:55 PM, Alex s wrote:
There was a typo in the last message, I found NO issues in point 2.
Actually, you did. You said when you removed the ions, the problem was
resolved. That indicates to me that the ions are somehow unstable. I don't
know much about doing CG simulations,
On 9/1/14, 3:26 AM, B P wrote:
Dear Gromacs users,
am trying to install gromacs 4.6.6 with GSL.
I have installed fftw3 and GSL in separate directories on Desktop and
linked them to Gromacs in the follwing command.
/home/user1/Desktop/cmake-2.8.12.2-Linux-i386/bin/ccmake ../ -DGMX_MPI=ON
On 9/1/14, 9:09 AM, nicola staffolani wrote:
Dear GROMACS community,
regarding this reported bug
http://permalink.gmane.org/gmane.science.biology.gromacs.user/66719 of
g_principal, I have edited gmx_principal.c in my
~/GROMACS/gromacs-4.5.5/src/tools folder as described, I have then left
On 9/1/14, 9:55 AM, Yorquant Wang wrote:
Hi,
Thank you for your reply. I have added the parameters from Slipid to
amber FF files (including: atomtypes.atp, ffbonded.itp, ffnonbonded.itp). I
also get such an error.
ERROR 1 [file ffbonded.itp, line 410]:
Not enough atomtypes (1
On 9/1/14, 10:45 AM, nicola staffolani wrote:
which substantially means this
http://www.gromacs.org/Documentation/Installation_Instructions#quick-and-dirty-installation,
right?
Install it however you normally do.
-Justin
2014-09-01 15:42 GMT+02:00 Justin Lemkul jalem...@vt.edu:
On 9
On 9/2/14, 10:49 AM, neha bharti wrote:
Thanks for your reply Justin
The error is now solve but I don't know this is a right way or not.
The step which I perform previously in which I am facing error:
Packing :
1) perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5
area_shrink1.dat
On 9/2/14, 10:52 AM, neha bharti wrote:
Hello All
I am trying to perform MD for protein ligand protein complex in popc lipid
with
charmm36 force field and also follow Justin A. Lemkul tutorial.
I also wanted to ask that while create special index groups consisting of
solvent + ions and
On 9/2/14, 10:13 PM, Kester Wong wrote:
Dear gmx-users,
I have manually created a graphene.itp file for charmm27 forcefield
calculations, with the intention to model the contact angle of water.
The atomic mass and charge values were obtained from the forcefield
ffnonbonded.itp.
Could
On 9/3/14, 12:46 AM, RINU KHATTRI wrote:
hello justin
i made tc_group for protein ligand and popc but i have merged
protein_ligand_popc and sol_cl i made only two group now im running
long simulation what can i do is this two tc_group can create the
wrong analysis.
No idea. I doubt it
On 9/3/14, 7:40 AM, Anitha wrote:
Can we analyse catalytic mechanism of an enzyme using the classical all
atom MD simulation.
No.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of
On 9/3/14, 7:52 AM, Mark Abraham wrote:
Hi,
That does indeed contradict the docs. Can you please file an issue at
http://redmine.gromacs.org and attach your inputs and command line, so we
can reproduce it?
I think this comes from the fact that the code uses clear_mat(fr.box) and then
only
On 9/3/14, 3:39 PM, Johnny Lu wrote:
it gives #abc.part0001.xyz.1# and then #abc.part0001.xyz.2#. I moved all
files that starts with #. Hope that works.
If a simulation is actively running, it does not need the files from any
previous parts. When starting a continuation run, you need the
On 9/4/14, 2:51 PM, Victor Sojo wrote:
Hi all!
We're trying to use a DPhPG (i.e. archaeal/non-standard) lipid bilayer on
CHARMM36.
I put the lipid into ParamChem, (having previously added hydrogens and
converted to mol2 format).
I then put the parameters into the merged.rtp file in the
On 9/4/14, 9:42 PM, Lyna Luo wrote:
Dear gmx experts,
I'm using g_wham version 5.0 to generate PMF from non-gromacs umbrella sampling.
Following the option -ip, I prepared all pdo files in one directory and gzip
them.
Then I run g_wham -v -ip *.gz -bins 400 -temp 300 -tol 0.1 -auto. The
On 9/5/14, 3:27 AM, Indu Kumari wrote:
Good afternoon,
No, if your system is showing some charge then it gives a note not an
error. So the reason is something else, check your .mdp file.
In this case, a fractional net charge of this magnitude indicates a serious
topology error. It is a
On 9/5/14, 2:50 AM, Christina Florina wrote:
Hi,
I have just started my work in MD and using Gromacs 5.0. I need
to use cyclohexane as my solvent instead of water. I generated the topology
file, .itp and .gro using PRODRG. I have successfully incorporated the .gro
file using
need help to resolve it.
Something doesn't add up. You will need to provide all of your files for
download via a file-sharing service to diagnose. A simple #include statement
and correct updating of [molecules] is all that is needed.
-Justin
On Fri, Sep 5, 2014 at 3:37 PM, Justin Lemkul
On 9/7/14 2:37 AM, Lyna Luo wrote:
Dear GMX experts,
I can not figure out how to make g_wham readin data from my pdo file below,
even though I tried different -b option and component selections. Please see
the error message below. Thank you so much! -L
# UMBRELLA 3.0
# Component
On 9/8/14 12:36 AM, Lyna Luo wrote:
Hi Justin,
The blank between lines are just from email format. I used only one window to
see if g_wham can readin my data, but I actually have 64 window. Please see the
error message below. Thanks again! -Lyna
GROMACS: gmx wham, VERSION 5.0
On 9/8/14 12:30 PM, Mahboobeh Eslami wrote:
hi GMX users
i have simulated the protein-ligand complex by gromacs. I've repeated the
simulation twice but i have get very different results. in one of the
simulations ligand separated from protein and stayed in the center of box.
I've checked
and
thus can only go in a .top) need to be deleted.
-Justin
On Fri, Sep 5, 2014 at 5:25 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/5/14, 7:10 AM, Christina Florina wrote:
Hi,
I have included the chx.itp file in the protein.top file already.
Checked with the molecule name (CHX
On 9/9/14 8:51 AM, Tim Stauch wrote:
Dear all,
I am currently trying to “mutate a protein by changing its backbone directly,
i.e. I am not interested in changing a specific amino acid against another (I’ve
found out that you can use VMD or Pymol for this purpose), but I am rather
of the stuff I pointed out was either (1)
syntactically incorrect or (2) not appropriate for the file format.
-Justin
On Tue, Sep 9, 2014 at 3:38 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/9/14 12:51 AM, Christina Florina wrote:
Hi,
I have included the link to my dropbox where I
On 9/9/14 5:09 PM, R.S.K.Vijayan wrote:
Hi Ansuman,
That is optional.
Generally speaking, no, it's not. The real truth lies in what the .mdp settings
are and what the intent of NPT is. If you don't pass the .cpt file to grompp
-t, you stand to lose much (or all) of the previous state
On 9/9/14 3:51 PM, Agnivo Gosai wrote:
Dear Users
I am trying to find the net charge at the physiological pH value for a
protein molecule (Thrombin) in my case and am wondering if it is possible
to use GROMACS for doing it.
I am very new to GROMACS and at present I have been going through
On 9/9/14 9:09 PM, Leandro Bortot wrote:
Dear users,
I did some simulations of organic molecules in solution to study how
they interact, but I'm facing some problems and your help would be greatly
appreciated.
Consider the following case: I simulated two copies of molecule AcO
On 9/10/14 4:29 PM, Mark Abraham wrote:
Hi,
On Wed, Sep 10, 2014 at 5:40 PM, Johnny Lu johnny.lu...@gmail.com wrote:
hmm. If that is the case, I have two questions.
1. Why gromacs doesn't adopt the method of measuring temperature as
described in the JCTC paper?
(
On 9/11/14 6:09 AM, Lovika Moudgil wrote:
Thanks for reply Lalit , Actually my system have citrate anion and I want
.itp for citrate and further I will use OPLA/SS force field!! It can't be
generated be pdb2gmx!!
The OPLS-AA strategy is generally similar to GROMOS - you can piece the
On 9/11/14 8:01 AM, shahab shariati wrote:
Dear gromacs users
When I see trajectory file using vmd, there is state showed in following link:
https://www.dropbox.com/s/g8i934atodrb7te/figure2.TIF?dl=0
in initial structure, all 4 drugs were inserted in water phase, in one side of
bilayer.
with more information. It's not so
much an advantage as it is a tactic to overcome problems in nonbonded schemes,
which are greatly reduced when using PME.
-Justin
On Wed, Sep 10, 2014 at 9:35 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/10/14 4:29 PM, Mark Abraham wrote:
Hi,
On Wed, Sep
On 9/11/14 8:49 AM, Christina Florina wrote:
Hi,
[ molecules ]
; Compound #mols
Protein_chain_A 1
CHX3414
Here no water molecules to replace but to neutralize the system I
need to replace the solvent ions. As you told I
On 9/11/14 9:40 PM, Batdorj Batsaikhan wrote:
Dear gmx users,
I want to check interaction between heavy atoms (Hg, Pb etc.) and a protein.
Can I simulate heavy atoms in our system? Thank you.
If you can find a force field that adequately describes such systems, sure. The
ones in Gromacs
On 9/12/14 6:11 AM, Namita Singh wrote:
i nwant to generate a log file for residue residue contact of a
protein-protein complex.I am using
g_hbond -s a.tpr -f c.xtc -r 0.55 -num hbond.xvg -g hbond.log -n
atom_index.ndx -contact
bt i am not getting any log file.
Do you get the other
even after giving the -g hbond.log?
A .log file is only written when generating maps with -hbm and -hbn.
-Justin
On Fri, Sep 12, 2014 at 5:41 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/12/14 6:11 AM, Namita Singh wrote:
i nwant to generate a log file for residue residue contact
On 9/12/14 2:28 PM, Agnivo Gosai wrote:
Dear Users
I am facing a problem while compiling the GROMACS source code in my
university cluster. I am laying down my installation procedure step by step
:-
1. Downloaded fftw 3.3.4
2. exported paths of C-compiler and Fortran-compiler
3. Used the
On 9/13/14 7:59 AM, shahab shariati wrote:
Dear Justin
you said The -trans option takes a vector where you specify the amount of
translation to apply
I do not know what vector should be considered in -trans option.
Well, what have you tried? You need to shift your system along z, the
On 9/14/14 8:43 AM, shahab shariati wrote:
Dear Justin
Thanks for your reply.
I inserted 4 drug molecules in close vicinity to the membrane surface
in water phase, in one side of bilayer (for example, top). In the
different frames of trajectory, some of drug molecules (one or two
drug
On 9/14/14 8:58 AM, shahab shariati wrote:
Dear Justin
I did MD simulation on the NPT ensemble:
pcoupl = Berendsen
pcoupltype = semiisotropic
ref_p = 1.0
In this condition, to solve this problem, what should I do?
I have already
On 9/14/14 9:52 AM, shahab shariati wrote:
Dear Justin
I did following:
trjconv -f *.xtc -s *.tpr -n *.ndx -o **.xtc -trans 6.46063 6.57889 9
Based on your reply*, *I translated all system along the z.
I used x and y according to box dimension.
I used 9, instead of z dimension
On 9/14/14 10:29 AM, shahab shariati wrote:
Dear Justin
Based on your previous reply, I used following:
trjconv -f *.xtc -s *.tpr -n *.ndx -o **.xtc -pbc mol –trans 0 0 7
When I see **.xtc using vmd, unfortunately, problem was not solved.
Please see the following link:
On 9/14/14 12:59 PM, Eric Smoll wrote:
Hello Johnny,
Thanks for the suggestion. I dumped the contents of CMakeError.log below. I
am not sure why the C compiler failed. The error occurs on directory
change? Later in the log, libmopac.a fails. Is this a static/shared problem?
What is your
On 9/15/14 12:36 AM, RINU KHATTRI wrote:
http://s48.photobucket.com/user/mittukhattri/library/?view=recentpage=1
hello gromacs users
I am working on protein complex with popc membrane i have been plot
two graph which is between time vs rmsd (backbone) ,rmsf in rmsf file
i didnt get time its
On 9/15/14 4:52 AM, shahab shariati wrote:
Dear Tsjerk
Thanks for your reply.
I think that there is another problem, except for visualization.
I obtained the Z coordinate (along the bilayer normal) of the center of
mass of the 4 drug molecules (violet, blue, red and green lines) and
DPPC
On 9/15/14 12:11 PM, shahab shariati wrote:
Dear Justin
Very very thanks for your time and consideration.
Excuse me for many questions.
I want to make sure my trajectory is valid and accurate for analysis and
then for writing related paper.
It is.
My last question is that can I use
901 - 1000 of 6606 matches
Mail list logo
