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.
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-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
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
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
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
I just confused with these options.
So please give me proper protocol.
Thank you in advance.
With best wishes and regards
Rama david,
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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
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
.
With best wishes and regards,
Rama david.
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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
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
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
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
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
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
to these.
These is most difficult but needed things in MD.
With best wishes and regards,
Rama David.
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to these.
These is most difficult but needed things in MD.
With best wishes and regards,
Rama David.
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. 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
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http
???
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
-- 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 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
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
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: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
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
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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
Hi GROMACS users,
I wish to study proteins behaviour,With the help of command
genbox -ci protein.gro -nmol no of protein .. -box box size
-o out put file -p topology file I am putting the four peptide
at random positions, but I need to put theem close enough so they
are forming at least one
Hi GROMACS user,
With the help of command
genbox -ci molecule name -nmol molecule no required
-o out put file -box dimension
I get the desired no of added protein to cell.
But I found that some part of protein is outside
the cell ..
Is such system is good for
Hi GROMACS friends,
I am trying to put to peptide close to each other..
with the help of -editconf -ci and -nmol option ,the peptide can be put
randomly at different location, but they are far apart.
To solve problem I proceed as follow...
1. I make gro file , with
Hi GROMACS friend,
Thank you Justin For guidance.
As I also doing your KALP-15 in DPPC tutorial,
In that you maintain remove initial periodicity of
DPPC..
What is means initial periodicity??
That is the reason I thought the peptides have
Initial periodicity.(As
Hi GROMACS specialist,
My MD run get crashed because of less
memory.
I given the command
mdrun -s prev.tpr -f prev.trr -e prev.edr -o prev.trr -g
prev.log -cpi -append -v
Now is my system is started from the initial time or from the time of
Dear GROMACS Friends,
my MD run get crashed , I foollow following command ..
mdrun -s protein_md.tpr -c protein_md.trr -e protein_md.edr -g
protein_md.log -cpi -append -v
the system respond in a way..
Fatal error:
The original run wrote a file called 'traj.trr' which is larger than 2 GB,
but
Hi GROMACS specialist,
I am using MARTINI forcefield,
My mdp file contain following parameter
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 90
gromacs output is
Step 0, time 0 (ps) LINCS WARNING
relative constraint
Hi ,
Thank you for help.
I solve my problem for LINCS error
But now I have another problem
after mdrun command
gromacs output
Making 1D domain decomposition 4 x 1 x 1
starting mdrun 'Martini system from nap.pdb'
5000 steps,100.0 ps.
step 0Segmentation fault
Please give the valuable
Dear GROMACS specialists,
How to convert Coarse Grain Martini
to FG martini on Gromacs 4.5.4 version .
( And how to compile the source given in Martini
home page with 4.5.4 version as they mention only
Gromacs 3.3.1 version)
Please give the valuable advice..
--
gmx-users
Hello
I am doing JUSTIN Protein-ligand tutorial.
I complete your Lysozyme tutorial before these one.
I complete tutorial upto the make-ndx
but after giving command grompp for nvt.tpr
production..
I get the following error
No molecule were defined in the system ,
I know somewhere
Hi Gromacs Specialist,
1. I need the help regarding the PCA
(Principle component analysis ).
If anyone can suggest me a good review
article and some tips how to analyse PCA result
I am very new to simulation study.
I read GROMACS manual, but I need
any review type article.
Dear Gromacs Specialists,
I am very novice to Molecular Simulation study.
I am using GROMACS 4.5.4 version .
I completed some GROMACS tutorials , I not found any
tutorial on Simulated Annealing..
If Any one know the link please give me it..
I make my protocol to work on
you
With Best Regards,
On Fri, Mar 16, 2012 at 7:10 PM, Justin A. Lemkul jalem...@vt.edu wrote:
rama david wrote:
Dear Gromacs Specialists,
I am very novice to Molecular Simulation study.
I am using GROMACS 4.5.4 version .
I completed some GROMACS tutorials , I not found
Hi Gromacs Specialist,
I want to study protein aggregation study.
1. after giving the command g_anaeig -v .. -s .. -f .. -first 1 -last
1 -nframe 100 -extr ev1.pdb
I got the pdb structure having 100 frame , but the structure have
erroneous bonds,
I try both VMD and pymol, but but get the
Hi Gromacs Specialist,
I want to study How the protein interact
with each other ??
I run one simulation with following MDP file option ..
comm_mode = Linear; remove center of mass
translation
nstcomm = 1 ;
affect my run ...which proparty I have to check ??
Thank you in advance..
On Sat, Mar 24, 2012 at 9:41 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 24/03/2012 11:06 PM, rama david wrote:
Hi Gromacs Specialist,
I want to study How the protein interact
with each other
HI Gromacs Friends,
I complete one simulation for 4 different molecule placed
apart
in box of dimension 4 4 4 ..
when I used the trajectory I saw the one molecule interact with each other
but they are
getting broken because of box..(Some part protruding from other side).
To see
Hi shima
Read the insttruction carefully ..
DELETE ALL THE LINE AND SUBSEQUENT LINES IN THE SECTION
Delete all the bellow line in that section...
It will surely solve your problem (As I also Face the same one )
with best wishes,
On Thu, Mar 29, 2012 at 11:23 AM,
Hi Gromacs users ,
as per the link given on gromacs website...
Introduction to Molecular Dynamics Simulations and
Analysishttp://nmr.chem.uu.nl/%7Etsjerk/course/molmod/- Tutorial for
performing and analyzing simulations of proteins. Includes
examples of many of the gromacs analysis tools and
PM, Justin A. Lemkul jalem...@vt.edu wrote:
rama david wrote:
Hi Gromacs users ,
as per the link given on gromacs website...
Introduction to Molecular Dynamics Simulations and Analysis
http://nmr.chem.uu.nl/%**7Etsjerk/course/molmod/http://nmr.chem.uu.nl/%7Etsjerk/course/molmod/
- Tutorial
...@anu.edu.auwrote:
On 29/03/2012 7:20 PM, rama david wrote:
Hi everybody ,
I run simulation of 4 same molecule keep apart in box
of 4 4 4 dimension ..( 71 atom in one molecule = 71 * 4 = total atom are
284 )
force field = gromacs96 53a6
COM (center of mass) infirmation
box boundary ,so they may close to each other enough ..
so is the simulation is wrong or right ...
2. Please could you tell me , What are the right parameter for the G96
53a6 force field ??
thank you a lot for help ..
On Thu, Mar 29, 2012 at 7:03 PM, rama david ramadavidgr...@gmail.comwrote
-- Forwarded message --
From: rama david ramadavidgr...@gmail.com
Date: Fri, Mar 30, 2012 at 8:31 PM
Subject: About g_energy analysis
To: Discussion list for GROMACS users gmx-users@gromacs.org
Hi Gromacs users ,
I have 4 molecule in system, I am study how are they interacting
Hi Gromacs Friends ,
I have 4 molecule system in water
Force field is G96 53a6 ..spc water molecule ..
How to find out relaxation time of my system ???
All suggestion are welcome ..
I saved trajectory after 0.2 ps ..
Thank you in advance
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Hi Ankita ,
The error is self-explanatory , and simple to interpret it.
You check the Topology file and see the last line that showing
added ions ...
What was your genion COMMAND LINE
Have a nice day
Rama
On Mon, Apr 2, 2012 at 3:19 PM, Erik Marklund er
Hi Gromacs friends,
When I given the command ...
pdb2gmx -f .. -o .. -p .. -ignh
I gate the following error..
--
Program pdb2gmx, VERSION 4.5.4
Source code file: /build/buildd/gromacs-4.5.4/src/kernel/pdb2top.c, line:
1070
Fatal error:
atom N
the way to tackle these problem???
With Best Wishes,
R.Davaid
On Thu, Apr 5, 2012 at 4:13 PM, Justin A. Lemkul jalem...@vt.edu wrote:
rama david wrote:
Hi Gromacs friends,
When I given the command ...
pdb2gmx -f .. -o .. -p .. -ignh
I gate the following error
, Mark Abraham mark.abra...@anu.edu.auwrote:
On 6/04/2012 9:05 PM, Mark Abraham wrote:
On 6/04/2012 8:27 PM, rama david wrote:
Hi Gromacs Friends and Justin ,
Thank you for reply and suggestion.
These is short part of my PDB .
ATOM 1 1H ACE 1 0.000 0.000 0.000
ATOM
HI all ,
sorry for above incomplete information ,
I change CH3 of ACE residue of my pdb file to CA .
Thank you in advance
On Fri, Apr 6, 2012 at 5:34 PM, rama david ramadavidgr...@gmail.com wrote:
Hi GROMACS Friends and Mark..
Thank you for reply ...
My command line is
pdb2gmx -f pdb
Hi Justin ,
Thank you , You are right .
Problem get solved by change in spacing in PDB file.
have a nice day.
With Best Wishes,
R.David
On Fri, Apr 6, 2012 at 6:36 PM, Justin A. Lemkul jalem...@vt.edu wrote:
rama david wrote:
HI all ,
sorry for above incomplete information ,
I change
Hi priya ,
I am also have same problem...
From my limited experience ..
To solve these problem it is a good way to make
index file of particular group (or molecule )
and then measure there g_mindist, g_gyrate and g_hbond
You can get gyrate and hbond value for them...
Have a nice Day ...
With
Hi Priya,
Check these link ..May be helpfull to you ,
http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering
From my limited Experience ,
I suggest ,you should have to make the group of
the molecule as per they forming micelle (As u get the 2-3 micelle )
,make 2-3 group by make_ndx
Hi sai,
you have to used docked structure to simulation .
1st convert the dock structure ,that you concider imptortant for
your further study to pdb file (As you used autodock for docking ).
Then perform MD on that structure.
Have a nice day...
On Thu, Apr 12, 2012 at 2:14 PM, sai nitin
Hi priya
http://www.gromacs.org/Documentation/Gromacs_Utilities/make_ndx these
link may be help to you
i like to know how to calculate index groups for my micelles..
since i am having two micelles , one having 8molecules and another having
2molecules.. residue number for that 2molecule micelle
Hi Sai,
you have to concider the protein and ligand strucure togather (Docked
structure ),
After these follow the link
(
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
)
With Best Wishes,
Rama
On Thu, Apr 12, 2012 at 5:13 PM, sai nitin sainit
priya thiyagarajan priya.thiyagaraja...@gmail.com wrote:
hello sir,
Thanks a lot for your help.. i got my own index file for my micelles using
make_ndx..
Thanking you,
Hi Priya,
Try g_spatial tools for micelle study,
http://www.gromacs.org/Documentation/Gromacs_Utilities/g_spatial
Hi Gromacs user ,
In justin tutorial protein-ligand complex..
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/08_MD.html
the production md.mdp has following parameter for Pressure and Temperature
coupling
; Temperature coupling is on
tcoupl = V-rescale
On Sat, Apr 14, 2012 at 6:12 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Hi Justin,
Thank you for reply..
My query is ..Why Pressure Coupling is off in production MD run ???
Pressure coupling is on, hence:
pcoupl = Parrinello-Rahman
That means sentence
; Pressure
not found
How to solve the error..
All suggestion are welcome..
Thank you in Advance...
Have a good day.!!!
With Best Wishes,
Rama David.
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, Apr 21, 2012 at 6:27 PM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 21/04/2012 9:27 PM, rama david wrote:
Hi Gromacs Friends,
I wish to apply charmff 27 to my protein and ligand
I proceed in following way ..
1. I separate the protein and ligand by grep command
then delete
HI vineetha,
On Sat, Apr 21, 2012 at 9:32 PM, vineetha mandlik vinee2h...@gmail.comwrote:
Respected Sir/Madam
I am new to gromacs and on giving the grompp command after genion command
I am getting the following error:
Even after running the genion command and adding 4 Na+ ions
, Please help me to know the best way to determine
hydrogen
bonds number in trajectory by Gromacs..
With Best Wishes,
Rama David
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3:23:40 PM
Subject: Re: [gmx-users] Check V for NVT
Rama G wrote:
Hi Gmx users,
I am using 4.0.X version of Gromacs and doing a NVT simulation. Now I wanna
check if the Volume is constant after the simulation.
I tried g_energy but did not find Volume in the pool of the options. Can
anyone
for NVT
On Fri, 13 Aug 2010 18:23:40 -0400
Justin A. Lemkul jalem...@vt.edu wrote:
Rama G wrote:
Hi Gmx users,
I am using 4.0.X version of Gromacs and doing a NVT simulation. Now
I wanna check if the Volume is constant after the simulation.
I tried g_energy but did not find Volume
Hi guys,
I got a little shocked when I used the -e and -dt in g_hbond, why the default
for - e is 0, on manual it says -e means last frame to read from
trajectory.
I know -b means First frame to read from trajectory with default 0, why do
both default values are the same, and both from 0.
Dear Gmxers,
I am working on a new project and I plan to do some molecular dynamic
simulation on an engineered GFP molecule. I have been searching for the
parameters for the GFP chromophore without success. Could some one help me? Any
reference or parameters will be appreciated.
Thanks,
Juju
position of DPPC was crossing the center of the lipid bilayer which is weird. Thanks Rama
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to run a hundred times, but I am not sure how to go about it. If anyone can provide me with pointers on that it would be greatThanks in advance Rama
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g_rotacf with -noaver?Will that compute the rotational correlation of the individual P-N vectors of each lipid molecule and average it over 128 molecules?Thanks in advanceRegardsRamaDavid van der Spoel [EMAIL PROTECTED] wrote: On Fri, 22 Sep 2006, Rama Gullapalli wrote:Hello everybody,I have nearly
it over 128 molecules?Thanks in advanceRegardsRamaDavid van der Spoel [EMAIL PROTECTED] wrote: On Fri, 22 Sep 2006, Rama Gullapalli wrote:Hello everybody,I have nearly 100 different vectors to analyse using g_rotacf. I was wondering if there was anyway to do this in GROMACS simultaneously since
Hello everybody.I have question regarding g_rotacfIf I wanted to compute the rotational correlation function of a linear vector which is between the "centers of masses" of two groups of atoms in an individual molecule (Instead of two atoms), how do I go about it?Can I use g_rotacf to do it ?Thanks
a lot Rama
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for it?Thanks a lotRama
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increasing the nrexcl to 5 in the N and P atoms ( to avoid intramolecular contributions?) And yet, I still get that spike. Any insight would be very helpful Thanks Rama
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as the autocorrelation of the angle wrt time?
Thanks for your time
Regards
Rama
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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
the
different barostat ant thermostat but still using the same Force field.
I am looking forward for reply.
With Best Wishes,
Rama David
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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
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..
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