Hi Gromacs users,
I'm doing protein-Bilayer MD simulations. Enzyme contains structural zinc
and calcium ions during Energy minimization, NVT and NPT stage, ions are
changing there position even though I applied position restraints for the
atoms and ions.
Anyone could help me out.
Thanks
--
Hi Justin,
Below I pasted .mdp file and topology. In .log file I could see energy term
for position restraints.
.mdp file---
title = NPT Equilibration
define = -DPOSRES ; position restraints for protein
; Run parameters
integrator = md
.
How to fix whole MD trajectory?
Thanks
Rama
--
View this message in context:
http://gromacs.5086.x6.nabble.com/Broken-lipid-molecules-tp5011344.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org
Hi ,
I there any tool to calculate distance between particular atom from one
group(protein) to particular atom from another group(DMPC lipid in Bilayer).
For Example: protein backbone Amide(HN) to acyl chain carbon atom(C2D) in
DMPC lipid.
Thanks
Rama
--
View this message in context:
http
:
Incorrect number of parameters - found 3, expected 2 or 4 for Bond.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
Thanks
--Rama
On Wed, Sep 11, 2013 at 6:47
CC2 35.26 334.72
C1A OE OF C1B2 0.00 167.36
C2A OG OH C2B2 0.00 167.36
Thanks
--Rama
On Thu, Sep 12, 2013 at 8:28 AM, Justin Lemkul jalem...@vt.edu wrote:
On 9/12/13 9:21 AM, Rama Krishna Koppisetti wrote:
Hi
[ bondedtypes ]
; Col 1: Type
) from starting
residue PHE100 (Protein).
Warning: Residue CA268 in chain has different type (Ion) from starting
residue PHE100 (Protein).
Thanks Justin .., I appreciate your help for whole week. I stopped here
(give up).
--Rama
___
Ramakrishna
2520 2521 31 0.00 3.773
2519 2520 2521 2524 31 0.00 3.193
2519 2520 2521 2522 3
2519 2520 2521 2523 3
2520 2521 2524 2525 31 0.00 3.193
Thanks
--Rama
Hi Justin,
Should I use R-B dihedrals for DMPC lipids rather than periodic
dihedrals.
I'm getting an Error message like,
ERROR 18815 [file topol.top, line 54180]:
No default Ryckaert-Bell. types
ERROR 18816 [file topol.top, line 54181]:
No default Ryckaert-Bell. types
--Rama
LC2 LH11 0.00 3.773
LOS LC2 LH1 LC21 0.00 5.923
LC2 LH1 LOSLC1 0.00 3.773
T
hanks
Rama
On Wed, Sep 11, 2013 at 8:17 AM, Justin Lemkul jalem...@vt.edu wrote:
On 9/11/13 9:05 AM, Rama Krishna Koppisetti wrote:
Hi Justin
Those lines are related to DMPC lipid dihedrals.
-_Rama
On Wed, Sep 11, 2013 at 8:17 AM, Justin Lemkul jalem...@vt.edu wrote:
On 9/11/13 9:05 AM, Rama Krishna Koppisetti wrote:
Hi Justin,
Should I use R-B dihedrals for DMPC lipids rather than periodic
dihedrals.
You should use
Sorry.., Justin
Yes.. It is a sequence of atom numbers from DMPC atoms. The errors are
coming from all DMPC atoms dihedrals only not by protein dihedrals.
--Rama
On Wed, Sep 11, 2013 at 9:08 AM, Justin Lemkul jalem...@vt.edu wrote:
On 9/11/13 10:06 AM, Rama Krishna Koppisetti wrote
---
I tried to look all the parameters in the .rtp file and ffbonded.itp and
ffnonbonded.itp files I don't find any mistake.
I hope you can help me
--Thanks
Rama
On Wed, Sep 11, 2013 at 9:16
, line 23515]:
No default Ryckaert-Bell. types
--Rama
On Mon, Sep 9, 2013 at 5:16 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/9/13 6:11 PM, Rama Krishna Koppisetti wrote:
Hi Justin,
I included 1 DMPC molecule parameters in the file should I need to include
128 molecules parameters
Hi Justin,
It is which part in the force field. Exactly which file I have to look to
overcome this errors.
Thanks
--Rama
On Tue, Sep 10, 2013 at 8:25 AM, Justin Lemkul jalem...@vt.edu wrote:
On 9/10/13 9:21 AM, Rama Krishna Koppisetti wrote:
Hi Justin,
This is another type of error
several multiplicity terms.
old: 0 5.09 2 0 5.09 2
new: LOSLP LOS LC21 0.00 3.193
Thanks
--Rama
On Tue, Sep 10, 2013 at 12:34 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/10/13 1:28 PM, Rafael I. Silverman y de la Vega wrote:
Adding parameters can
Hi,
How to convert normal dihedrals to so-called Ryckaert-Bellemans
potential dihedrals. Is there any script available for that.
Thanks
Rama
On Tue, Sep 10, 2013 at 3:44 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/10/13 4:35 PM, Rama Krishna Koppisetti wrote:
H
i Justin,
The force
H
i Justin,
The force field that I constructed with OPLS + Berger lipids
.
Similar to
your Bilayer tutorial.
Thanks
--Rama
On Tue, Sep 10, 2013 at 3:26 PM, Rama Krishna Koppisetti
ramkishn...@gmail.com wrote:
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org
Ok..I got it
Thanks Justin...
--Rama
On Mon, Sep 9, 2013 at 1:49 PM, Rama Krishna Koppisetti
ramkishn...@gmail.com wrote:
Hi Justin ,
I prepared .rtp files for lipid. what is the exact command to merge two
chains in gromacs.
On Fri, Sep 6, 2013 at 4:37 PM, Justin Lemkul jalem
Hi Justin ,
I prepared .rtp files for lipid. what is the exact command to merge two
chains in gromacs.
On Fri, Sep 6, 2013 at 4:37 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/6/13 5:35 PM, Rama Krishna Koppisetti wrote:
H
i Justin,
Thanks for your reply.
How to do
Hi Justin,
I included 1 DMPC molecule parameters in the file should I need to include
128 molecules parameters in the file .rtp.
Thanks
--Rama
On Mon, Sep 9, 2013 at 4:43 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/9/13 5:37 PM, Rama Krishna Koppisetti wrote:
Hi Justin,
I merge two
Hi Justin,
I merge two molecules as a single molecule type. Now I'm trying to do
energy minimization of the system, getting errors like
Fatal error: [file topol.top, line 55130]:
No default Proper Dih. types
Any idea for this type of errors.
Thanks
--Rama
On Mon, Sep 9, 2013 at 1:57
Hi Justin,
I use similar procedure as you mentioned in the tutorial to generate my
topologies for protein and bilayer. there is no .rtp file for lipid. Is
there any reference to include lipid molecule in aminoacid.rtp file.
Thanks
Rama
On Fri, Sep 6, 2013 at 4:57 PM, Justin Lemkul jalem
Hi Justin,
If you are willing to see my complex pdb file or complex .gro file and
topology files, I'll send you for the reference.
Thanks
Rama
On Sat, Sep 7, 2013 at 5:42 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/7/13 6:40 PM, Rama Krishna Koppisetti wrote:
Hi Justin,
I use
1.0
14258216 1 8 1 0.0
1.52462.0791.0
On Fri, Sep 6, 2013 at 4:23 PM, Rama ramkishn...@gmail.com wrote:
Hi,
I'm doing NMR restrained MD simulation for protein-Bilayer system to
satisfy
NMR experimental data.
Without
Hi,
I'm doing NMR restrained MD simulation for protein-Bilayer system to satisfy
NMR experimental data.
Without restraints there is no problem, but if I include distance restraints
in topology file, getting fatal error:
the lipid atom index # was not recognized by using this command:
g_grompp
H
i Justin,
Thanks for your reply.
How to do that?
On Fri, Sep 6, 2013 at 4:27 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/6/13 5:23 PM, Rama wrote:
Hi,
I'm doing NMR restrained MD simulation for protein-Bilayer system to
satisfy
NMR experimental data.
Without restraints
Hi Justin ,
Is there any script available in gromacs documentation or some where?
Thanks
On Fri, Sep 6, 2013 at 4:37 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/6/13 5:35 PM, Rama Krishna Koppisetti wrote:
H
i Justin,
Thanks for your reply.
How to do that?
If .rtp entries
Hello,
At NPT stage the two leaflets in DMPC bilayer is separated a while and comes
closer. Is this common in this stage or any thing goes wrong in
equillibration.
Thanks
--Rama
--
View this message in context:
http://gromacs.5086.x6.nabble.com/DMPC-Bilayer-tp5010783.html
Sent from
else.
--Rama
--
View this message in context:
http://gromacs.5086.x6.nabble.com/DMPC-Bilayer-tp5010685.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please
the
different barostat ant thermostat but still using the same Force field.
I am looking forward for reply.
With Best Wishes,
Rama David
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org
tau_p= 1
NVT parameter are same.
On these basis can I make the interpretation that XX form beta sheet
structure early than YY
though they uses the same barostat but different tau_P ??
With Best Wishes and Regards,
Rama David
On Sat, Jul 20, 2013 at 4:49 PM, Justin Lemkul jalem...@vt.edu
-dump 0 -sep
Thanks in Advance.
Rama
On Mon, Jul 15, 2013 at 2:02 AM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:
look for either -dt or -skip.
Dr. Vitaly V. Chaban
On Mon, Jul 15, 2013 at 2:03 AM, Rama ramkishn...@gmail.com wrote:
Hi,
How to get a snapshots in equal intervals
Thank you very much *Justin*.
--
Rama
On Mon, Jul 15, 2013 at 8:06 AM, Justin Lemkul jalem...@vt.edu wrote:
On 7/15/13 9:02 AM, Rama Krishna Koppisetti wrote:
Hi,
The following command I used for the snapshots but I'm getting one frame
time 0 time 500. what are the changes I need
Thanks *Thomas*
--Rama
On Mon, Jul 15, 2013 at 9:00 AM, Thomas Schlesier schl...@uni-mainz.dewrote:
Hi,
the following:
trjconv -s md.tpr -f md.trr -o beta.gro -dt 250 -sep
should work.
-dt 250 ; write output every 250 ps
-sep ; to write each frame (but the output frequency gets
Hi,
I saved my coordinates every 500ps in production MD run, could I alter now
.xtc file by saving different coordinates for ex: every 100ps. Is there any
command to alter the files.
Thanks in Advance
--Rama
--
View this message in context:
http://gromacs.5086.x6.nabble.com/How-to-make
O
kay...
T
hanks for prompt reply *Justin*
*
.
--Rama
**
*
On Mon, Jul 15, 2013 at 11:11 AM, Justin Lemkul jalem...@vt.edu wrote:
On 7/15/13 12:08 PM, Rama wrote:
Hi,
I saved my coordinates every 500ps in production MD run, could I alter now
.xtc file by saving different coordinates
Hi,
How to get a snapshots in equal intervals of time (250ps) from production MD
trajectory. I'm using -sep , -t0, -timestep but output came only one .gro
file.
--
View this message in context:
http://gromacs.5086.x6.nabble.com/snapshot-tp5009837.html
Sent from the GROMACS Users Forum
Dear All,
I'm trying to do long stimulation run but every time it stops at 2ns, below
pasted .mdp file parameters. How to run 10ns or more ns stimulation run? Do
I need to change any parameters in .mdp file or else where.
Thanks in Advance.
-
title = Protein-DMPC bilayer
:
On 7/8/13 4:33 PM, Rama wrote:
Dear All,
I'm trying to do long stimulation run but every time it stops at 2ns,
below
pasted .mdp file parameters. How to run 10ns or more ns stimulation run?
Do
I need to change any parameters in .mdp file or else where.
There is nothing in the .mdp file
Hi Friends,
I am working on peptide self assembly.
I simulated two peptide which are random coil and apart from each other.
As the time process they start to interact and form antiparallel beta sheet
structure.
My plan is to find the energy difference in random coil to beta
shhet
Dear Gromacs users,
How to define distance restraints between two molecules(protein and a lipid)
in a topology file.
Thanks..
--
View this message in context:
http://gromacs.5086.x6.nabble.com/Distance-restraints-tp5008421.html
Sent from the GROMACS Users Forum mailing list archive at
what.)
Mark
On Tue, May 21, 2013 at 4:20 PM, Rama ramkishn...@gmail.com wrote:
Dear Gromacs users,
How to define distance restraints between two molecules(protein and a
lipid)
in a topology file.
Thanks..
--
View this message in context:
http://gromacs.5086.x6
Hi..,Mark
but it is within the same molecule , not in inter-molecules.
On Tue, May 21, 2013 at 11:36 AM, Mark Abraham mark.j.abra...@gmail.comwrote:
Yes. Check out the manual first!
Mark
On Tue, May 21, 2013 at 5:16 PM, Rama Krishna Koppisetti
ramkishn...@gmail.com wrote:
Hi Mark
Hi,
I'm new to Gromacs. How to convert NMR paramagnetic relaxation enhancement
distance restraints into gromacs format in topol.top file for structural MD
refinement.
--Rama
--
View this message in context:
http://gromacs.5086.x6.nabble.com/Distance-Restraints-tp5008207.html
Sent from
g_sham -h, I tried it, but not understand properly)
I will be very grateful for your suggestion and help..
With Best Wishes,
Rama David
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org
Dear
http://folding.bmc.uu.se/remd/ this may help you.
With best regards
On Thu, Apr 4, 2013 at 11:43 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com
wrote:
Dear all,
We are stuck at the last stage of running a successful REMD.
We have obtained average potential energy by fitting the
..
With best Regards
Rama david.
On Thu, Apr 4, 2013 at 1:56 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/4/13 2:14 AM, rama david wrote:
Dear Friends,
I simulated the 4 peptide in water box .
As they come close to each other they start to from anti-parallel
beta sheet structure.
Now
g_sham -h and manual.
Please accept my apology.
I will be grateful to you for help ...
With best regards,
Rama david.
On Thu, Apr 4, 2013 at 6:24 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/4/13 5:50 AM, rama david wrote:
Thank you justin,
I read the articles, archive and also
Dear Justin,
Thank you a lot for help and kind passion to listen me.
I finally come with the my desired out put.
I
I am grateful to you for help.
With Best Wishes,
Rama david
On Thu, Apr 4, 2013 at 7:09 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/4/13 9:37 AM, rama david wrote
that are possible to implement in
my work flow.
I will be very grateful to you for your help and suggestion.
With Best Regards,
Rama David
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org
:45 PM, massimo sandal deviceran...@gmail.comwrote:
I would look on some paper which temperature ranges and conditions
(NPT/NVT) were used for systems of a similar size and with a similar aim.
2013/4/2 rama david ramadavidgr...@gmail.com
Dear friends ,
Thank you justin and Mark for your
Thank you justin.
I will do the same.
On Tue, Apr 2, 2013 at 10:06 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/2/13 9:24 AM, rama david wrote:
Thank you Massimo sandal, Justin and mark ,
I also goes through the article and GMX archive.
But I confuse with the protocol ( I am naive
.
With Best Wishes and Regards,
Rama David.
On Tue, Jan 8, 2013 at 12:55 PM, mohammad agha mra...@yahoo.com wrote:
Dear GROMACS Specialists,
I have one system consists of many surfactant molecules that they create
several micelles. How should I know that time of simulation is enough
-- Forwarded message --
From: rama david ramadavidgr...@gmail.com
Date: Wed, Dec 26, 2012 at 9:55 PM
Subject: About g_enemat problem
To: gmx-users-ow...@gromacs.org
Hi Gromacs friend.
I simulated a system containing random peptide
I found that as they start to interact
???
With Best Wishes and regards,
Rama david
On Wed, Nov 28, 2012 at 6:03 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/28/12 12:20 AM, rama david wrote:
Hi justin,
Thank you for your suggestion.
I read the ATB paper but the paper does not mention any thing related to
the biotin.
Probably
Hi justin,
Thank you for help
With Best wishes and Regards,
Rama david
On Wed, Nov 28, 2012 at 7:09 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/28/12 8:08 AM, rama david wrote:
Hi justin thank you for suggestion.
I think to Calculate the free energy of solvation of biotin, I hve
to these.
These is most difficult but needed things in MD.
With best wishes and regards,
Rama David.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting
. Biotin was
not a part of the validation dataset.
What should I have to do..???
Please give me the suggestion.
With best wishes and regards,
Rama david
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http
to these.
These is most difficult but needed things in MD.
With best wishes and regards,
Rama David.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting
atoms in the
system. The output group can be the whole or part of the calculation group.
As two protein comes closer in simulation they formed the antiparrallel
beta strand, I want to find the change in hydrophilic and hydrophobic
surface area of protein...
With Best Wishes and Regards,
Rama david
Thank you justin
With best wishes and regards,
Rama David
On Fri, Nov 23, 2012 at 12:45 AM, Justin Lemkul jalem...@vt.edu wrote:
On 11/22/12 1:54 PM, rama david wrote:
Hi justin,
Thank you for reply.
As per your suggestion,
The whole protein should always
Dear,
-o MT.PnoH.xtc instad of xtc extenstion use pdb you will get pdb file.
And then load it in vmd or pymol u can see it
On Wed, Nov 21, 2012 at 10:24 PM, Rausch, Felix frau...@ipb-halle.dewrote:
Hi.
Try to load in a .gro file of your system first. After that, use the load
data into
on these topics.
Is there any free available software for these work???( I never did any QM
calclation, Sorry for these basic Question).
With Best Wishes and Regards,
Rama David.
On Thu, Nov 15, 2012 at 8:23 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/15/12 9:47 AM, rama david wrote
Should I need to corret charge ...???
On Thu, Nov 15, 2012 at 11:51 PM, rama david ramadavidgr...@gmail.comwrote:
Hi Justin thank you,
The ATB server link for Biotin are as follow..
http://compbio.biosci.uq.edu.au/atb/download.py?molid=5783
compbio.biosci.uq.edu.au/atb/download.py?molid
Thank you for your reply.
On Sun, Nov 11, 2012 at 8:30 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/11/12 4:51 AM, rama david wrote:
Hi justin ,
Thank you a lot for your explaination.
My opinion on the working of g_mindist -pi is that when it shows the
distance between two atom
to check the protein pbc , I have to make the
index file for each chain, and have to select the pbc for that???
Please accept my apology if I repiting the same questions. but it is
really confusing to me..
With best Wishes and Regards..
Rama david
On Sun, Nov 11, 2012 at 12:47 AM, Justin Lemkul
.
With best wishes and regards,
Rama david.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list
Dear ali,
the tutorial link you given used the G43a1 ,
The opls-AA and G43a1 paramete4r are different.
To choose the right parameter for system is a very important step in
simulation.
With best wishes and regards,
Rama david
On Sat, Nov 10, 2012 at 12:10 PM, Ali Alizadeh
ali.alizadehmoja
with these result
With best wishes and regards,
Rama david.
On Sat, Nov 10, 2012 at 6:55 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/10/12 5:42 AM, rama david wrote:
Dear expert,
I am simulating the protein-ligand system.
Mdp file parameter are
Neighborsearching
ns_type = grid
Hi justin,
If you dont mind please give the link for gromacs 4 paper , it will surely
help
me to decide ff and parameter...
Thank you in advance,
With best wishes and regards,
Rama david
On Sat, Nov 10, 2012 at 6:58 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/10/12 7:09 AM, Ali Alizadeh
10.7
So please would you told me the reason for my g_mindist value less than vdw
cut off 1.4 ?
With best wishes and regards,
Rama david
On Sat, Nov 10, 2012 at 7:26 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/10/12 8:44 AM, rama david wrote:
Hi justin ,
Thank you for reply
be the problem if I used the whole group
Still I not get the your explanation..Pardon me, but please explain it
again??
On Sat, Nov 10, 2012 at 8:34 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/10/12 10:02 AM, rama david wrote:
Dear justin,
Thank you for your reply and explanation,
My
Dear Rajeswari,
May I ask you why you want to do the multiple protein simulation.??
Please mention the purpose clearly, otherwise it is hard to understand
what you are doing and what you need???,
With best wishes and Regards,
Rama David
On Fri, Nov 2, 2012 at 3:22 PM, Rajeswari
thank you..
On Fri, Nov 2, 2012 at 3:56 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/2/12 1:13 AM, rama david wrote:
Dear all,
I am running a system with sol 40646 atom and ion, NA 629 CL 634.
At the time of nvt and npt should i have to make different *tc_grps* for
ion and sol
Dear all,
I am running a system with sol 40646 atom and ion, NA 629 CL 634.
At the time of nvt and npt should i have to make different *tc_grps* for
ion and sol or should be make one group
Nonprotein ( these include sol + ion)..these is default.
With Best wishes and regards,
Rama david
--
gmx
I just confused with these options.
So please give me proper protocol.
Thank you in advance.
With best wishes and regards
Rama david,
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org
Thank you for your reply,
Are these Cg can be used in Gromacs.
Thank you in advance.
With best wishes and regards,
Rama david
On Wed, Oct 10, 2012 at 6:13 PM, XAvier Periole x.peri...@rug.nl wrote:
Martini FF cannot model changes in secondary structure ... other CG FF
can. You'll find
Hi thank you
Please told me the name of Freely available software on which these FF can
be used ..
Thank you in advance
With best wishes and regards,
Rama david
On Wed, Oct 10, 2012 at 6:26 PM, XAvier Periole x.peri...@rug.nl wrote:
Nope, but on other softwares.
On Oct 10, 2012, at 2
the interaction energy.
As the MD need a lot of time , you can´t use it for the large library.
I plan to do only 5 simulation.
With best wishes and regards.
Rama david
On Wed, Oct 10, 2012 at 6:54 AM, Justin Lemkul jalem...@vt.edu wrote:
On 10/9/12 9:17 PM, Liu Shiyong wrote:
Justin,
Single
Segmentation fault (core dumped)
What is the reason ???
thank you in advance.
With best wishes and regards
Rama david.
On Sat, Oct 6, 2012 at 6:47 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/6/12 6:26 AM, rama david wrote:
Hi justin,
I tried as per your suggestion.
command line
and regards
Rama david
On Mon, Oct 8, 2012 at 3:06 PM, Albert mailmd2...@gmail.com wrote:
Dear:
I am using the command:
trjconv -f md.trr -s md.tpr -dump 54000 -o md.pdb -pbc mol
trjconv -f md.pdb -s md.tpr -o fit.pdb -fit rot+rans
to extract a frame of my md simulation and I found my
50001 frames
Segmentation fault (core dumped)
On Mon, Oct 8, 2012 at 3:22 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/8/12 5:40 AM, rama david wrote:
Hi justin,
As per your advice,
g_enemat -f ener.edr -groups groups.dat -nocoul -nolj
Opened ener.edr as single precision energy
fault (core dumped)
Thank you in advance
Rama david.
Let me be a bit more specific again. I previously suggested there was a
problem with the -lj flag activating more than one option in the code, so
that is a potential problem. I suggested adding -nolj -coul to test this
theory. Please use
reference temperature for free energy
calculation )
Any suggestion on these topic, is helpful to me.
Thank you in advance,
With best wishes and regards,
Rama david.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search
-matrix of 2 groups, 3 elements, over 50001 frames
Segmentation fault (core dumped)
why program not work ?? Is it bug??? or Am I doing any stupid mistake???
Thank you in advance ..
With best wishes and regards,
Rama david
On Sat, Oct 6, 2012 at 3:40 PM, Justin Lemkul jalem...@vt.edu wrote
Hi justin,
I completed the simulation ,
Now I want to use the selected residues of protein and ligand.
How to do it
Would you explain me in detail??
With best wishes and regards,
Rama david.
On Fri, Oct 5, 2012 at 3:40 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/5/12 5:49 AM, rama david
Hi justin,
thank you for reply.
With best wishes and regards
Rama david.
On Fri, Oct 5, 2012 at 4:07 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/5/12 6:15 AM, rama david wrote:
Hi justin,
I completed the simulation ,
Now I want to use the selected residues of protein and ligand
have
to choose ??
What is Lamb-energy???
Is I did any mistake??? or I have to use any else command ??
Thank you in advance
With best wishes and regards.
Rama david.
On Fri, Oct 5, 2012 at 7:54 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/5/12 10:16 AM, rama david wrote:
Hi gromacs
Hi justin,
Ok now I get
I have to modify mdp parameter ..
Thank you,
With best wishes and regards,
Rama david
On Fri, Oct 5, 2012 at 9:47 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/5/12 11:46 AM, rama david wrote:
Thank you for your Help.
I did the following tc-groups
tcoupl
you in advance.
With best wishes and regards,
Rama david
On Fri, Oct 5, 2012 at 10:32 PM, rama david ramadavidgr...@gmail.comwrote:
Hi justin,
Ok now I get
I have to modify mdp parameter ..
Thank you,
With best wishes and regards,
Rama david
On Fri, Oct 5, 2012 at 9:47 PM, Justin
Essential Dynamics ??? or Principle component analysis ???
Would you suggest me any general protocol for such work??
Thank you in Advance
With Best Wishes and regards.
Rama David
On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/4/12 2:01 AM, rama david wrote:
Hi
should have same effect..Am I right or wrong??
If you have any other way please suggest it..
With best wishes and regards
Rama david
On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri
francesco.ot...@gmail.comwrote:
Hi,
as far as I know, freezing just set velocities to 0 so you gain nothing
idea.
Is any other way to do the same thing..
With best wishes and regards
Rama David
On Thu, Oct 4, 2012 at 5:47 PM, francesco oteri
francesco.ot...@gmail.comwrote:
2012/10/4 rama david ramadavidgr...@gmail.com
Hi francesco,
Thank you For reply.
I did docking but the result are not so
in advance
Thank you for giving your valuable time and advice to me.
With best wishes and regards,
Rama david
On Thu, Oct 4, 2012 at 6:11 PM, Thomas Evangelidis teva...@gmail.comwrote:
I don't think AutoDock and Vina are suitable for peptide docking. I would
first try the FlexPepDocking module
Hi Deepak,
Is the gromacs is in your path??
Please mention your operating system..
With best wishes and Regards,
rama david
On Thu, Oct 4, 2012 at 11:07 AM, Deepak Ojha alwaysinthem...@gmail.comwrote:
Dear All
I want to use Amber force field in Gromacs therefore I installed the
latest
)..
Please, would you tell me another way to solve these problem..??
Thank you in advance
Have a nice day.
Rama David
On Tue, Oct 2, 2012 at 8:28 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/2/12 7:07 AM, rama david wrote:
Hi Gromacs Users,
I did simulation
Dear Ravi
Use trjconv -dump ... ( time in ps)
With Best wishes and regards
Rama david.
On Mon, Oct 1, 2012 at 11:15 AM, Ravi Kumar Venkatraman
ravikumarvenkatra...@gmail.com wrote:
Dear All,
How to get a snapshot at a particular time frame from the MDS
run.
Thank
Yes it will work ..
Just at the time of mdrun add -cpi cpt ( prvious cpt file )
With best wishes and regards..!!
On Sun, Sep 30, 2012 at 8:48 AM, Acoot Brett acootbr...@yahoo.com wrote:
Dear All,
for my original MD, based on mdp file the total time is 500 ps. After it
finished, I have
you in advance..
With best wishes and regards
Rama David
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe
1 - 100 of 229 matches
Mail list logo
