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
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
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
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
.
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.
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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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to these.
These is most difficult but needed things in MD.
With best wishes and regards,
Rama David.
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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.
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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
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
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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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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.
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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
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
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...here md.gro
through browse open the md.xtc then load it..
With best wishes aned regards..
Rama david
On Wed, Aug 15, 2012 at 3:27 PM, Acoot Brett acootbr...@yahoo.com wrote:
Dear All,
I just installed a VMD. And then I load a gro file and a xtc file from a
simulation. The bar in the VMD
Sorry md.pdb/md.gro
On Thu, Aug 16, 2012 at 11:34 AM, rama david ramadavidgr...@gmail.com wrote:
Hi
do the following ..
open the trajectory in tthe molecule not as seperate molecule..
As example you havre md.gro and md.xtc files..
file == new molecule
load files for md.pdb open
-ordinates or something else)
I get confused
Please accept my apology for stupid question
Please help to come out through the confusion.
With best wishes and regards
Rama david
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on Gromacs 4.5.4
With best wishes and regards,
Rama David
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With best wishes and regards
Rama David..
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Justin,
Thank you for your reply,
I check the manual but it is giving only small information..
I would be greatly thankfull to you if you shed some light on
these option ...
With best wishes and regards
Rama David
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.??
Is there any way to find out which option to use when
How all the things going to affect the result
I goes trough archive but not find satisfactory answer...
I am looking for clear and simple explanation...
Thank you in advance..
With Best wishes and regards
Rama david
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file: No such file or directory
I have a small experience in linux only, That why I may be missing or
done something wrong???
So please tell me where is the problem
Thank you in advane..
With Best wishes and regards,
Rama david.
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http
Hi Gromacs Friends,
I am trying to install gromacs 4.5.4 in parallel operating system fedora 17
I am using dell T 3500 precision , 6C.
I downloaded openmppi-1.6
Command line to install
./configure --prefix=/usr/local
make all install
For fftw 3.3.2 installation command line was .
Precision T 3500 )...
With best Wishes and Regards...
Rama David
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So what is wrong???
With best wishes and regards
Rama david
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and regards
Rama David
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output is it able to perform REMD or not ?
Is the gromacs installation on my system is right for open-mpi
With Best Wishes and regards
Rama david
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and regards.
Rama David
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thank you for immediate reply...
Suppose, If I installed from Fedora software packages
How to check that Gromacs installed in Parallel version and can
performed REMD
Thank you in Advance..
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Thank you M.ark..
I got following reply..
Fatal error :
mdrun -multi is not supported with thread library .Please compile
gromacs with MPI support.
I have to try to compile gromacs as per the webpage instructions...
With best wishes and regards..
Rama David..
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in advance.
Have a nice Day.
With best wishes and regards,
Rama David
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Hi Gromacs Friends,
I completed the Justin Protein KALP - lipid tutorial ...
I want to simulate the DPPC lipid bilayer membrane under
Stress condition ( Lateral tension = 20 mNm/m)..
For stress condition I made the following npt.mdp
; Temperature coupling is on
tcoupl =
Dear cuong nguyen..
I think use following commands.
Try editconf -rotate for rotaion angle along axis
along these use -center co-ordinate if you want to place canter of
box at particular position
Try editconf -translate For translation along axis
On Tue, Jul 17, 2012 at 2:07 PM, Mark
???)
Please give me the valuable suggestion in these regard
Thank you in advance.
Have a nice Day.
With best wishes and regards,
Rama David
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( Perpendicular press ) ???
( Why to say P|| = -30 Pz = 1 , will give the teral tension of
20 mNm/m ???)
Please give me the valuable suggestion in these regard
Thank you in advance.
Have a nice Day.
With best wishes and regards,
Rama David
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Hi Gromacs Friends,
I have the experimental result of change in Secondary
structure of peptide from random coil to Beta sheet, as the conc
increases
( but not know the Parallel or anti-parallel )
I run Simulation of ( 30ns ) two peptide in random coil
structure
Thank you Justin for your Explaination
Please Would you me the Reason Why these parameter is present in
Equilibration mdp and
not in production run mdp file ( for both lysozyme and lipid simulation )
With Best Wishes and regardsRama
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simulation???
How to check these parameter affect my result sensitivity???
Please give me valuable guidance to solve my query..
With Best Wishes and regards,
Rama David
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Please search
Hi Gromacs Friends,
I completed Justin-Lipid Tutorial.
I plan to simulate protein-lipid system to study protein-lipid interaction.
My Query is like
1. I plan to use DPPC (128) lipid from Tieleman Website.
I removed its periodicity as per tutorial instruction..
I found that I need the z box
On Tue, Jun 26, 2012 at 9:32 PM, rama david ramadavidgr...@gmail.com wrote:
Hi Gromacs Friends,
I completed Justin-Lipid Tutorial.
I plan to simulate protein-lipid system to study protein-lipid interaction.
My Query is like
1. I plan to use DPPC (128) lipid from Tieleman Website.
I
Hi Gromacs Friends,
I am doing Justin-lipid tutorialer
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html
In these the npt.mdp has a parameter
refcoord_scaling = com
Why these parameter is introduced in NPT of lipid-protein simulation
and not use in Lysozyme in
310 310 323 300 310
Thank you in advance
With Best Wishes,
Rama David
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Hi Gromacs Friends,
I did NPT for 100 ps with folowing parameter
; Temperature coupling is on
tcoupl= V-rescale; modified Berendsen thermostat
tc-grps= Protein Non-Protein; two coupling groups - more
accurate
tau_t= 0.10.1; time constant, in ps
ref_t
THANK YOU Justin,
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On Tue, Jun 12, 2012 at 4:40 PM, rama david ramadavidgr...@gmail.comwrote:
Hi Gromacs Friends,
I did NPT for 100 ps with folowing parameter
; Temperature coupling is on
tcoupl= V-rescale; modified Berendsen thermostat
tc-grps= Protein Non-Protein; two coupling
thank you for Quick reply
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is restrained and the sidechain is free to
move, So I
think it may be help to achieve my goal.
After these I also plan to use SA as production run, then compare the
result with previous protocols.
Please give valuable suggestion to improve my study protocol..
With Best Wishes,
Rama David
Thank you for reply
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But Truly I dont Want to change the arrangment (distance 0.5 nm),
Please Help me to solve the above problem,
All suggestion are welcome
With Best Wishes,
Rama David
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in z direction, Such that separation in each
layer is 0.4 ,
I arranged eight layer in Z direction(total 24 peptide 8 * 4=32 ),
All things was right.
Thank you in Advance
With Best Wishes,
Rama David
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reason )
last option :
you have a single water molecule somewhere within the system that is
isolated from the other water molecules.
How to find such water molecule and solve the problem??
Thank you in Advance .
With Best Wishes,
Rama David
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Hi Justin, thank you for quick reply.
You are right I have practicle result, And I want to replicate them..
Thank you for your suggestion..
With Best Wishes,
Rama David
On Mon, Jun 11, 2012 at 3:58 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 6/11/12 6:23 AM, rama david wrote:
Hi Mark
run, users give .cpt file as input to -mdrun,
My query is, There are two cpt file a) pre.cpt b) .cpt ,
So which one has to given as input???
All suggestion are welcome...
With Best Wishes,
Rama david
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Thank you Justin for quick reply
On Sat, Jun 2, 2012 at 8:12 PM, Justin A. Lemkul jalem...@vt.edu wrote:
To perform these task I am using following command
1. grompp -f New mdp file just change in saving output -t .cpt -c
.gro
file(gro file from position restrained run ) -o
Thank You for Quick reply Justin...
On Sat, Jun 2, 2012 at 8:58 PM, Justin A. Lemkul jalem...@vt.edu wrote:
You'll get a mismatch in your files (checkpoint, trajectory, energy) in
terms of frame interval. You should not try to append to these files or
extend the run. Just run a new
choose total 28 windows instead of 23 ...So is it good or bad ???
Thank you in Advance...
With Best Wishes,
Rama David
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