On Tue, May 8, 2012 at 1:01 PM, rama david ramadavidgr...@gmail.com wrote:
On Tue, May 8, 2012 at 1:00 PM, rama david ramadavidgr...@gmail.comwrote:
Hi Gromacs user,
I am doing the justin tutorial on lipid posted on link..
On Mon, May 7, 2012 at 5:11 PM, Sarath Kumar Baskaran
bskumar.t...@gmail.com wrote:
First i had simulation of the protein alone in united atom gromacs force
field by -ff gmx in pdb2gmx
now i am unable to run the protein-ligand complex for the same protein
with a ligand,
it says the
On Mon, May 7, 2012 at 10:17 AM, Bala S think_bey...@aol.com wrote:
Justin and Anirban,
I have another query on membrane simulation following your tutorials.
How do I insert only a part of protein into the lipid bilayer and carryout
the simulation?
editconf with -box option helps you to
On Thu, May 3, 2012 at 4:38 PM, scapr...@uniroma3.it wrote:
Hi all,
I'm new in Membrane simulations with Gromacs. I have to simulate a system
made up of a protein just leant on a membrane patch which has previously
been extended and made it free of periodicity (with trjconv). I'm reading
the
On Thu, May 3, 2012 at 5:17 PM, Weingarth, M.H. m.h.weinga...@uu.nl wrote:
Hello,
I am a bit confused by a comment which I find in all MARTINI example
md.mdp scripts concerning the tc-groups :
It is stated there to couple groups separately:
MARTINI -Normal temperature and pressure
Hi ALL,
I am simulating a membrane protein immersed in a POPC bilayer using
CHARMM36 FF in GROMACS 4.5.5. In NVT and NPT (i.e. in equilibration and
production runs) should I use the dispersion correction or not (as
suggested in some previous posts)?
And if NOT using dispersion correction, then
Hi ALL,
I was looking for a CHARMM36 format (atom-types) equilibrated POPC bilayer
(PDB/GRO) to use with the CHARMM36 FF in GROAMCS 4.5.5. I downloaded one
from Dr. Klauda's site (
http://terpconnect.umd.edu/~jbklauda/research/download.html), but that
popc.pdb (under CHARMM36 FF) seem to have
Receptor Model Simulations
Front. Gene.
Volume 3 Year 2012 Number 61
DOI: 10.3389/fgene.2012.00061
On 2012-05-02 05:49:17PM +0530, Anirban Ghosh wrote:
Hi ALL,
I was looking for a CHARMM36 format (atom-types) equilibrated POPC
bilayer
(PDB/GRO) to use with the CHARMM36 FF in GROAMCS
Hi ALL,
I have a equilibrated POPC bilayer (100 ns run) that I have run using
GROMOS ff53a6 FF. Now, I wish to use this POPC bilayer for a new simulation
using CHARMM36 FF in GROAMCS 4.5.5. There are differences in atom naming
conventions (N, P, C, O) between this two FFs as a result of which
, Anirban Ghosh wrote:
Hi ALL,
I have a equilibrated POPC bilayer (100 ns run) that I have run using
GROMOS
ff53a6 FF. Now, I wish to use this POPC bilayer for a new simulation
using
CHARMM36 FF in GROAMCS 4.5.5. There are differences in atom naming
conventions
(N, P, C, O) between
On Mon, Apr 30, 2012 at 11:50 AM, seera suryanarayana
paluso...@gmail.comwrote:
Respected Sir,
While i am running the gromacs software to simulate
the protein i am getting the following error.
Fatal error:
Residue 'GNP' not found in residue topology database
On Sat, Apr 28, 2012 at 10:22 PM, Andrew DeYoung adeyo...@andrew.cmu.eduwrote:
Hi,
Typically, I use Gromacs 4.5.5 compiled with automatic threading. As you
know, automatic threading is awesome because it allows me to start parallel
runs without calling mpirun. So on version 4.5.5, I can
On Fri, Apr 27, 2012 at 1:01 PM, Bala S think_bey...@aol.com wrote:
Dear Justin
Thanks for the explanation.
I am following your tutorial of KALP membrane simulation. I am stuck in
between two steps of InflateGRO. After the first step, the tutorial
requests
to perform EM. Should I be
On Fri, Apr 27, 2012 at 3:17 PM, seera suryanarayana paluso...@gmail.comwrote:
Respected Sir,
While i am running gromacs software i am getting the
following error.Kindly knowing me how to over come the error.
Fatal error:
On Fri, Apr 27, 2012 at 3:27 PM, Bala S think_bey...@aol.com wrote:
Thank you for that clarification.
I found that there were SOL molecules in .top file. I could run the EM now.
Coming to the Solvation step, I'm facing a problem.
I have made the mentioned change (0.15 to 0.375 for C) in
On Fri, Apr 27, 2012 at 4:59 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 4/27/12 6:40 AM, Bala S wrote:
Thanks for the reply.
I'm following the tutorial.
Please clarify whether you're using Anirban's or mine. Now that two
exist, people will have to be a fair bit more specific :)
On Fri, Apr 27, 2012 at 6:31 PM, Bala S think_bey...@aol.com wrote:
Justin,
OOPS!!
Sorry for that.. Now I could realize it.
Following up.. I have done further iterations with inflategro and reached
0.62 nm^2 which similar to what you have explained in the tutorial.
Now, I could see the
On Fri, Apr 27, 2012 at 7:00 PM, Bala S think_bey...@aol.com wrote:
Anirban,
Thank you. You guys are doing miracles with the biomolecules and solving
almost all of my problems.
I have followed your suggestion and could see now some more SOL molecules
by
increasing the z value.
But I am
On Fri, Apr 27, 2012 at 7:37 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 4/27/12 10:00 AM, Bala S wrote:
Anirban,
Exactly.. That's the gap (either side of the leaflets) I was mentioning
about. I'll try EM and check itagain.
EM won't fill in solvent gaps. If you're using my protocol
Hi ALL,
I have prepared a step-wise tutorial for running a MD simulation of a GPCR
protein inserted in a lipid bilayer. I sincerely hope it will help people
who are new to such simulations and the GROMACS community in general. This
tutorial is adapted from the membrane protein tutorial prepared
Hi ALL,
I have prepared a step-wise tutorial for running a MD simulation of a GPCR
protein inserted in a lipid bilayer. It can be found at the following URL:
https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial
I sincerely hope it will help people who are new to such simulations and
Hi ALL,
I have prepared a step-wise tutorial for running a MD simulation of a GPCR
protein inserted in a lipid bilayer. It can be found at the following URL:
https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial
I sincerely hope it will help people who are new to such simulations and
it is the best FF for lipids currently.
On 04/26/2012 11:14 AM, Anirban Ghosh wrote:
Hi ALL,
I have prepared a step-wise tutorial for running a MD simulation of a
GPCR protein inserted in a lipid bilayer. It can be found at the following
URL:
https://sites.google.com/site/anirbanzz/gpcr
1u ns belongs
to this range? CHARMM36 ff is available in gromacs website and we can
download it and put them into top directory and then it works. It is not
need to make any modification by ourselves.
best
Albert
On 04/26/2012 11:53 AM, Anirban Ghosh wrote:
Hello Albert,
Thanks.
Yes
Albert
On 04/26/2012 12:59 PM, Anirban Ghosh wrote:
Hello Albert,
Good to know that!
I have carried out simulations using this FF in the range of 600 ns.
Regards,
Anirban
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp
Hello Bala,
Yes, exactly as Justin said it represents just a workflow where a GPCR
protein (here B2AR) has been taken as an example. I mentioned it as a GPCR
tutorial because many often inquire about GPCR MD simulations only in the
forum. But it can be adapted for other membrane proteins as well.
Hi ALL,
When running a membrane protein (say GPCR) in a lipid bilayer (say POPC or
DPPC etc.) which according to your experience is the most suited
force-field in GROMACS that best retains the 7TM / secondary structures of
the protein over long simulations? I have tried running with ff53a6 (as
-adrenergic receptor system.
On 2012-04-19 12:02:36PM +0530, Anirban Ghosh wrote:
Hi ALL,
When running a membrane protein (say GPCR) in a lipid bilayer (say POPC
or
DPPC etc.) which according to your experience is the most suited
force-field in GROMACS that best retains the 7TM
Hello Justin,
In your membrane protein simulation tutorial after making the topology, you
have mentioned that Placing the new gromos53a6_lipid.ff directory in
$GMXLIB will allow you to use this force field system-wide. I suppose this
is valid only for the proteins (and not membranes) to be
Hello Peter,
Thanks a lot for clarifying my doubt!
I have got it right now.
Thanks,
Anirban
On Thu, Dec 8, 2011 at 3:34 PM, Peter C. Lai p...@uab.edu wrote:
On 2011-12-08 02:43:13AM -0600, Anirban Ghosh wrote:
Hello Justin,
In your membrane protein simulation tutorial after making
Hi ALL,
Is it possible to run constant pH MD simulation (CPHMD) in Gromacs4.5?
Any suggestion is welcome.
Thanks,
Anirban
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
Hi ALL,
I am using in calculating the distribution of a solvent around the COM of a
protein chain using g_rdf. When I plot the output file (attached) I get a
curve which increases first (from 1 to a value of about 2.5) and then
decreases to x-axis values ranging from 1 to 5. If I understand
Hi ALL,
I have simulated a CGMD system consisting of multiple copies of a CG protein
in a CG lipid bilayer using the MARTINI FF for the CG definitions. Can I use
GridMatMD program to calculate the area per lipid and other properties in
this CG system? Which parameters do I need to alter in the
of some PBC issue. What
-pbc options should I use to generate a proper .gro file to be used as input
for GridMatMD?
Thanks a lot again.
Regards,
Anirban
On Mon, May 30, 2011 at 4:40 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Anirban Ghosh wrote:
Hi ALL,
I have simulated a CGMD system consisting
Hi ALL,
I have a long simulation trajectory of 3 micro-seconds of multiple protein
monomers in a lipid bilayer.
Which -pbc option should be used with trjconv to process the trajectory
before carrying out any analysis? I am using -pbc nojump, is it correct? Or
should I use -pbc whole?
Thanks a lot
. But the procedure is right.
Cheers,
Tsjerk
On May 7, 2011 7:35 AM, Anirban Ghosh reach.anirban.gh...@gmail.com
wrote:
Hi ALL,
I want to calculate the SASA of a protein embedded in a bilayer along with
water and ions. So while using g_sas I understand that I need to supply all
non-solvent atoms
and Protein as the output
group?
Thanks again,
Anirban
On Sat, May 7, 2011 at 1:05 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 7/05/2011 4:36 PM, Anirban Ghosh wrote:
Hello Tsjerk,
Thanks for the reply.
But if I consider the ions also in the calculation group, then it is not
wrong
Hi ALL,
I want to calculate the SASA of a protein embedded in a bilayer along with
water and ions. So while using g_sas I understand that I need to supply all
non-solvent atoms as calculation group and Protein as the output group. So I
need to make a group with Protein+Lipid+Ions as the
Hi ALL,
I am trying to use trjcat -f input files -o output_file to join to very
larger trajectories. However I am getting the following error:
---
Continue
---
So gmxcheck does not show any warning/error.
Then why I am getting the warning from trjcat. And how to remove it?
Thanks,
Anirban
On Thu, May 5, 2011 at 7:19 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Anirban
PM, Justin A. Lemkul jalem...@vt.edu wrote:
Anirban Ghosh wrote:
Hello Justin,
Thanks for the reply.
gmxcheck on the first trajectory shows:
-
Checking file protein_3000NS_2.trr
trn version
Hi,
I have successfully converted my CG (only) protein model to FG model using
g_fg2cg command of the gromacs_reverse package. But now when I try to
compile my .mdp file for SA run, grompp is throwing some warnings:
creating statusfile for 1 node...
Back Off! I just backed up mdout.mdp to
Hi,
I am trying to convert a CG system containing multiple copies of a protein +
lipid + water + ions to an all-atom system using the special gromacs_reverse
version command g_fg2cg. However I am getting the error:
at 12:01 PM, Anirban Ghosh
reach.anirban.gh...@gmail.com wrote:
Hi,
I am trying to convert a CG system containing multiple copies of a
protein +
lipid + water + ions to an all-atom system using the special
gromacs_reverse
version command g_fg2cg. However I am getting the error
410288
Number of cg atoms 57296
Reading frames from gro file 'Protein in DSPC Bilayer', 57296 atoms.
Reading frame 0 time0.000 1297343010
Segmentation fault
Why is this happening?
Thanks,
Anirban
On Thu, Feb 10, 2011 at 5:45 PM, Anirban Ghosh
reach.anirban.gh...@gmail.com wrote
Hi ALL,
Can anyone please send me an all-atom DSPC .itp file at *
reach.anirban.gh...@gmail.com *or* anirba...@gmail.com*
*
*
Thanks a lot.
-Anirban
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
Hi,
I am trying to convert a coarse grained protein to a full atom model after
CGMD. I am using the modified gromacs_reverse code available from MARTINI
site. I am using the following command:
g_fg2cg -pfg topol_fg.top -pcg pro_cg.top -n 0 -c pro_cg.gro -o full.gro
But in the output full.gro
Hi ALL,
Can anyone please send me an all-atom DSPC .itp file at *
reach.anirban.gh...@gmail.com *or* anirba...@gmail.com*
*
*
Thanks a lot.
-Anirban
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
to do this? And why am I getting
only a single value of DGbind for all the frames captured in the .edr file?
Thanks a lot.
Anirban
On Mon, Dec 27, 2010 at 11:51 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Anirban Ghosh wrote:
Thanks Justin for the reply.
I have through the threads about
On Tue, Dec 28, 2010 at 6:24 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Anirban Ghosh wrote:
Thanks a lot Justin for the reply.
So I ran a simulation with my ligand in water for 1 ns and using g_energy
I calculated the LG-14 and Coulomb-14 values from the .edr file. I supplied
the average
Thanks a lot Justin !!!
--Anirban
On Tue, Dec 28, 2010 at 11:03 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Anirban Ghosh wrote:
Thanks a lot Justin for the reply.
Yes I am going through all the relevant literature on LIE.
Actually the lie.xvg file contains the same value of -25.4
PM, Justin A. Lemkul jalem...@vt.edu wrote:
Anirban Ghosh wrote:
Thanks a lot Justin for the reply.
Yes I am going through all the relevant literature on LIE.
Actually the lie.xvg file contains the same value of -25.4 for all the
frames. So I am getting a straight line plot. Why
, 2010 at 11:45 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Anirban Ghosh wrote:
Thanks a lot Justin for the reply !!!
While calculating the Elj and Eqq values should we consider the
short-ranged LJ (LJ-SR) or LJ-14, the two components that are present in
1-4 interactions
Hi ALL,
Is there any means to calculate the total energy arising due to the breaking
and formation for hydrogen bonds only in GROMACS?
Does the .edr file contains this information? If yes then how to parse it? I
don't think the .log file records this value.
Any suggestion is welcome.
Thanks,
?
Thanks a lot.
Anirban
On Sat, Jul 17, 2010 at 4:56 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Anirban Ghosh wrote:
Hi ALL,
I have run a protein + ligand (dopamine) simulation. Now I want to
calculate the free energy of binding using g_lie. But g_lie asks for two
values: Elj and Eqq. How
picture of what has happened
to my protein at the end of the simulation. Should I use the first .tpr file
or the last .tpr file?
Thanks a lot again.
Anirban
On Fri, Dec 3, 2010 at 7:35 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Anirban Ghosh wrote:
Hi ALL,
Its a very basic question
this which .tpr file should I supply to trjconv, the first one or the
last one?
Thanks again.
Anirban
On 12/4/10, Justin A. Lemkul jalem...@vt.edu wrote:
Anirban Ghosh wrote:
Thanks a lot Justin for the reply. Yes, I understand that. But ideally
which structure should be used as the reference
should I use?
Thanks,
Anirban
On Sat, Dec 4, 2010 at 12:29 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 4/12/2010 4:33 PM, Anirban Ghosh wrote:
Thanks a lot for the reply.
Actually I am running a protein in lipid bilayer. Now I want to
calculate the thickness of the bilayer at the end
Hi ALL,
I am trying to run free energy calculation and for that in the md.mdp file I
am keeping the following option:
; Free energy control stuff
free_energy = yes
init_lambda = 0.0
delta_lambda= 0
sc_alpha=0.5
sc-power=1.0
sc-sigma= 0.3
But still I find
Hi ALL,
I am trying to run free energy calculation and for that in the md.mdp file I
am keeping the following option:
; Free energy control stuff
free_energy = yes
init_lambda = 0.0
delta_lambda= 0
sc_alpha=0.5
sc-power=1.0
sc-sigma= 0.3
But still I find
.
Regards,
Anirban
On Sat, Nov 27, 2010 at 9:15 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Anirban Ghosh wrote:
Hi ALL,
I am trying to run free energy calculation and for that in the md.mdp file
I am keeping the following option:
; Free energy control stuff
free_energy = yes
Hi ALL,
I have carried out REMD simulation on a protein (20 replicas). Now I want to
carry 2D PMF calculation using RMSD and Radius of gyration as the reaction
coordinates using Grossfield Lab's WHAM package. For this what should be my
input parameters to the WHAM program and in which format?
Any
code or there is some other way?
Any suggestion is welcome. Thanks again.
Regards,
Anirban
On Thu, Sep 16, 2010 at 5:28 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Anirban Ghosh wrote:
Hi ALL,
I have carried out REMD simulation on a protein (20 replicas). Now I want
to carry 2D PMF
The Bioinformatics Group at C-DAC, Pune is going to organize a Symposium on
Accelerating Biology from December 14-16 2010 at VITS, Pune. You can
register for the same at:
http://pune.cdac.in/html/events/bioinfo/accelerating_biology/index.aspx
Regards,
--
Anirban Ghosh
C-DAC, Pune, India
Hi ALL,
I have made a CGMD system with multiple copies of a single protein in
bilayer, by replicating the monomer using genconf in the X-Y plane. After
running CGMD for about 100 ns, I am getting the following error:
the curvature of your bilayer is not
responsible for the error message you are seeing.
to solve the problem you have to increase to use the -rrd option
(see manual for explanation). Typicaly a value of 1.4 to 1.6 should
be fine.
On Aug 16, 2010, at 12:16 PM, Anirban Ghosh wrote:
Hi ALL,
I have
Hi ALL,
I am trying to simulate a protein inserted in a lipid bilayer with water and
ions, the entire system built using CG (coarse grain). I am using the
Martini force field to the CGMD simulation. My question is that should I use
the centre of mass removal component in my .mdp file (which we do
:00 AM, Anirban Ghosh wrote:
Hi ALL,
I am trying to simulate a protein inserted in a lipid bilayer with water
and ions, the entire system built using CG (coarse grain). I am using the
Martini force field to the CGMD simulation. My question is that should I use
the centre of mass removal
Hi ALL,
I have run a protein + ligand (dopamine) simulation. Now I want to calculate
the free energy of binding using g_lie. But g_lie asks for two values: Elj
and Eqq. How or from where can I get these values for my ligand? Also, do I
need to run a simulation with only the ligand? And, is there
Hi ALL,
I have run a protein + ligand (dopamine) simulation. Now I want to calculate
the free energy of binding using g_lie. But g_lie asks for two values: Elj
and Eqq. How or from where can I get these values for my ligand? Also, do I
need to run a simulation with only the ligand? And, is there
Hi ALL,
I have run a protein + ligand (dopamine) simulation. Now I want to calculate
the free energy of binding using g_lie. But g_lie asks for two values: Elj
and Eqq. How or from where can I get these values for my ligand? Also, do I
need to run a simulation with only the ligand? And, is there
Hi ALL,
I have a system consisting of protein+lipid+ligand+water which has been
simulated for 10 ns. Now I want to make a compressed trajectory from the
original one by keeping only the protein and the ligand. I am trying to do
so by using trjconv with an index file. But every time trjconv is
,
Your 150 degree angle is in reality 30 degrees (180-30). This is a matter
of defining the vector representing your helix vs. the direction of the z
axis. If your vector points in the opposite direction of the z axis, then
your angle will be between 90 and 180 degrees.
George
Anirban Ghosh wrote
Thanks a lot XAvier!
On Sat, Jun 5, 2010 at 2:10 PM, XAvier Periole x.peri...@rug.nl wrote:
Yes,
or inverse your sections from the index!
On Jun 5, 2010, at 10:10 AM, Anirban Ghosh wrote:
Thanks XAvier and George for the reply. Yes the N and C terminus are on
the opposite sides
Hi ALL,
I am using g_angle to calculate the tilt of individual helix in a rhodopsin
GPCR with respect to z axis. In the index file I am defining the top and
bottom of each helix with first 4 and last 4 residues of that helix
respectively. Strangely, I am getting the tilt angle of the odd helices
Hi ALL,
I tried to calculate the helix tilt of a single helix (TM5) among 7 helices
using g_bundle. In the index file I defined the two groups (top bottom) as
the C-alpha of the first 5 and last 5 residues of TM5 respectively. But in
the bun_tilt.xvg file I am getting the values as:
Hi ALL,
I am trying to find out the tilt of a helix during a simulation. I am using
g_helixorient with the -otilt option. However I am getting the following
output, which when plotted using xmgrace, gives a straight along y=0.
Hi ALL,
I am trying to find out the tilt of a helix during a simulation. I am using
g_helixorient with the -otilt option. However I am getting the following
output, which when plotted using xmgrace, gives a straight along y=0.
Hi ALL,
I am trying to find out the tilt of a helix during a simulation. I am using
g_helixorient with the -otilt option. However I am getting the following
output, which when plotted using xmgrace, gives a straight along y=0.
Hi ALL,
I tried to calculate the helix tilt of a single helix (TM5) among 7 helices
using g_bundle. In the index file I defined the two groups (top bottom) as
the C-alpha of the first 5 and last 5 residues of TM5 respectively. But in
the bun_tilt.xvg file I am getting the values as:
Hi ALL,
I tried to calculate the helix tilt of a single helix (TM5) among 7 helices
using g_bundle. In the index file I defined the two groups (top bottom) as
the C-alpha of the first 5 and last 5 residues of TM5 respectively. But in
the bun_tilt.xvg file I am getting the values as:
Hi ALL,
I want to calculate the distance between a number of atom pairs using
g_dist. For this I want to submit the job through a submission script so
that g_dist calculates the distances for all the pairs one after the other.
But I need to select the two groups from an index file. How can I give
Hi ALL,
I want to calculate the distance between a number of atom pairs using
g_dist. For this I want to submit the job through a submission script so
that g_dist calculates the distances for all the pairs one after the other.
But I need to select the two groups from an index file. How can I give
Thanks a lot Justin.
On Tue, May 18, 2010 at 4:36 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Anirban Ghosh wrote:
Hi ALL,
I want to calculate the distance between a number of atom pairs using
g_dist. For this I want to submit the job through a submission script so
that g_dist
Hi ALL,
I am trying to do a PCA for my simulation. I generated a covarience matrix
using g_covar and now I want to visualize the motion only along first
principal component. So with g_anaeig I gave the option -first 1 -last
1. But it gave the error as:
Hi ALL,
I am trying to do a PCA for my simulation. I generated a covarience matrix
using g_covar and now I want to visualize the motion only along first
principal component. So with g_anaeig I gave the option -first 1 -last
1. But it gave the error as:
Hi ALL,
How can I obtain the residence time of each hydrogen bond during a
simulation? I think the -hbn and -hbm options of g_hbond has to be used, but
how? Is there any script to extract that data? And what is the difference
between the residence time and the life time of a hydrogen bond? Any
Hi ALL,
How can I obtain the residence time of each hydrogen bond during a
simulation? I think the -hbn and -hbm options of g_hbond has to be used, but
how? Is there any script to extract that data? And what is the difference
between the residence time and the life time of a hydrogen bond? Any
Hi ALL,
I just want to convert my trajectory (.trr) to a compressed .xtc format
after removing water from it. trjconv has to be used for this. I just want
to know should I use an index file to exclude the water from the trajectory
or is there any other option to be given with trjconv to write out
with it.
Can you please guide me regarding this and also please go through the other
parameters in the .mdp file.
Regards,
Anirban
On Wed, Apr 28, 2010 at 4:52 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Anirban Ghosh wrote:
Hello Justin,
In my topology file I am declaring
On Thu, Apr 29, 2010 at 3:29 PM, Saumya samvygu...@gmail.com wrote:
Hi all,
I am using the pre-equilibriated layers from Tieleman. After the first
energy minimization step, I removed the periodicity using trjconv. Now, in
order to scale the lipid positions, I tried using Inflategro.
Do I
with it.
Can you please guide me regarding this and also please go through the other
parameters in the .mdp file.
Regards,
Anirban
On Wed, Apr 28, 2010 at 4:52 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Anirban Ghosh wrote:
Hello Justin,
In my topology file I am declaring
I making? And how can I freeze properly the helical portions and
simulate only the loop? Thanks a lot in advance.
Regards,
Anirban
On Fri, Apr 23, 2010 at 5:37 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Anirban Ghosh wrote:
Hi ALL,
I want to do a MD simulation by restraining (freezing
with it.
Can you please guide me regarding this and also please go through the other
parameters in the .mdp file.
Regards,
Anirban
On Wed, Apr 28, 2010 at 4:52 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Anirban Ghosh wrote:
Hello Justin,
In my topology file I am declaring
Hi ALL,
This may sound like a very basic question, but I am still pondering over it.
I have simulated a membrane protein system for 30 ns after Steepest Descent
minimization and now I want to perform NMA. From the help pages what I
understand is that I need a very well minimized system (using
Hi ALL,
This may sound like a very basic question, but I am still pondering over it.
I have simulated a membrane protein system for 30 ns after Steepest Descent
minimization and now I want to perform NMA. From the help pages what I
understand is that I need a very well minimized system (using
I making? And how can I freeze properly the helical portions and
simulate only the loop? Thanks a lot in advance.
Regards,
Anirban
On Fri, Apr 23, 2010 at 5:37 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Anirban Ghosh wrote:
Hi ALL,
I want to do a MD simulation by restraining (freezing
Hi ALL,
I want to do a MD simulation by restraining (freezing) the helical portions
and allowing only the loop regions to move. I tried doing this by applying
heavy restrain on the helical residues by generating a .itp file with the
genrestr command with an index file containing the desired
Hi ALL,
I have a ligand LDOPA with 25 atoms (including all hydrogens).:
---
DAH COORDS
25
1DAH O1 5.988 5.216 9.128
1DAH C2
are not explicitly modeled.
you should be able to erase those from your gro file, but I would
suggest you get into some literature about the FF you use.
XAvier.
On Apr 14, 2010, at 11:36 AM, Anirban Ghosh wrote:
Hi ALL,
I have a ligand LDOPA with 25 atoms (including all hydrogens
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