Dear all,
This may sound stupid, but just to make sure that I am right track about
implicit solvent simulations, the set up involves
pdb2gmx
editconf
grompp
I mean, we still need to define the box dimensions by editconf and apply
periodicity, right?
Besides, what type of ensemble would be a good
I fixed it ... but now after using the command : grompp -f em.mdp -c
solv.gro -p topol.top -o ions.tpr
I am getting a charge of -9.71e-01
Since the charge has to be in whole number, what shall I do in this case.
(The ligand that I am using is phosphotyrosine)
On Tue, Jun 21, 2011 at 2:13
On 21/06/2011 3:43 PM, Kavyashree M wrote:
Sir,
I am extremely sorry for this question again :(
but I wanted to know this violation exists only in
first 50ns but after that even though there appears
to be a point of violation its only 1.39nm which is
o0.01nm less than the cut off which I
So, after adding 1 NA ion, I started with energy mimization, but I am
getting the following error after md run command :-
Step=1, Dmax= 1.0e-02 nm, Epot= 1.36889e+09 Fmax= 1.97591e+11, atom=
1248
Step=2, Dmax= 1.2e-02 nm, Epot= 5.46814e+07 Fmax= 3.57239e+09, atom=
972
Step=3, Dmax=
Dear users,
When are checking the cosine content of a PC, (Pls. Correct me if I am
wrong)
This is the command we use -
g_analyze -f input-principle-component.xvg -cc outputcosine
content.xvg
and for first PC output says -
Cosine content of set 1 with 0.5 periods: ---
for nth PC also it says
On 21/06/2011 4:15 PM, bharat gupta wrote:
I fixed it ... but now after using the command : grompp -f em.mdp -c
solv.gro -p topol.top -o ions.tpr
I am getting a charge of -9.71e-01
Since the charge has to be in whole number, what shall I do in this
case. (The ligand that I am using is
On 21/06/2011 4:33 PM, bharat gupta wrote:
So, after adding 1 NA ion, I started with energy mimization, but I am
getting the following error after md run command :-
Please search for help first.
http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
Mark
Step=1,
Hi
How to calculate RMSD per residue with Gromacs ?
Thank you
Lin
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Please don't post
Hi Shahab,
When comparing two variables, they have to share an axis. Time for instance...
Cheers,
Tsjerk
On Tue, Jun 21, 2011 at 6:36 AM, shahab shariati
shahab.shari...@gmail.com wrote:
Dear Tsjerk
thanks for your attention.
larger radius of gyration, more surface. and smaller radius of
E. Nihal Korkmaz wrote:
Dear all,
This may sound stupid, but just to make sure that I am right track about
implicit solvent simulations, the set up involves
pdb2gmx
editconf
grompp
I mean, we still need to define the box dimensions by editconf and apply
periodicity, right?
Not usually.
Chih-Ying Lin wrote:
Hi
How to calculate RMSD per residue with Gromacs ?
g_rmsf -od
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu |
Dear Tsjerk
very thanks for your useful guidance.
I now know that I should compare output of g_gyrate (containing Rg vs time)
by area.xvg output file of g_sas (containing area vs time).
In area.xvg output file, there are several columns: Hydrophobic,
Hydrophilic and Total.
for example in time,
Hi,
I am a new user in gromacs and i would like to create a plot from several
.xvg files. Can anyone guide me through the process?
Thank you in advance
N.V.
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Please search the archive at
On 21/06/2011 7:40 PM, Nicole Varvarigou wrote:
Hi,
I am a new user in gromacs and i would like to create a plot from
several .xvg files. Can anyone guide me through the process?
That's not really the purpose of this list, which is for GROMACS-related
questions. I can suggest that you look
You understand correctly.
On Tue, Jun 21, 2011 at 11:35 AM, shahab shariati
shahab.shari...@gmail.com wrote:
Dear Tsjerk
very thanks for your useful guidance.
I now know that I should compare output of g_gyrate (containing Rg vs time)
by area.xvg output file of g_sas (containing area vs
Hi Nicole
In linux/unix, there are a program named xmgr aor xmgrace by default.
Just you type in command line : xmgr 1.xvg 2.xvg 3.xvg ..
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
--
gmx-users mailing
Dear Gromacs Users,
I've done Justin's tutorial regarding PMF/umbrella sampling and now, when
approaching my own system I have a couple of questions.
(Link to the tutorial here:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html)
My system is
Shay Teaching wrote:
Dear Gromacs Users,
I've done Justin's tutorial regarding PMF/umbrella sampling and now,
when approaching my own system I have a couple of questions.
(Link to the tutorial here:
Thanks for you prompt reply! Clear and to the point.
-Shay
On Tue, Jun 21, 2011 at 2:03 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Shay Teaching wrote:
Dear Gromacs Users,
I've done Justin's tutorial regarding PMF/umbrella sampling and now, when
approaching my own system I have a couple
I want to obtain solvent accessible surface area using g_sas command:
g_sas -f *.xtc -s *.tpr -n *.ndx -o -or -oa.plz tell me the full
command as i am getting error while running this command.thanx in
advance!!
how I will obtain three output files containing: area.xvg, resarea.xvg
and
Dear Gromacs community
I would like to better understand how the uncertainty on the
diffusion coefficient is calculated in GROMACS.
I am calculating water diffusivity for different water models at
different temperatures.
I am using Gomacs 4.5.4
Reading the manual, I am a bit
rashi parihar wrote:
I want to obtain solvent accessible surface area using g_sas command:
g_sas -f *.xtc -s *.tpr -n *.ndx -o -or -oa.plz tell me the full command as i
am getting error while running this command.thanx in advance!!
To get an answer you need to provide an actual command
thanx justin..my problem is that i do not know exactly the syntax of
command.i get to know about this command through this community only.i.e why
i want the full command?
On Tue, Jun 21, 2011 at 6:53 PM, Justin A. Lemkul jalem...@vt.edu wrote:
rashi parihar wrote:
I want to obtain solvent
rashi parihar wrote:
thanx justin..my problem is that i do not know exactly the syntax of
command.i get to know about this command through this community only.i.e
why i want the full command?
Please read the contents of the manual about g_sas and/or g_sas -h for a full
list of options
Can anyone comment further on either of these issues?
-Justin
Mark Abraham wrote:
On 15/06/2011 4:24 AM, Justin A. Lemkul wrote:
Hi All,
I wanted to dig up an old discussion that hit the list a long time ago
because I'm now encountering some problems understanding the GB
settings myself.
Dear Prema:
1. Do you think my e-mail is an alias for gromacs mailing list, please? I am
not sure.
2. What about downloading the manual and referring yourself to the section
where topology files are described?
Enjoy gromaxing...
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ.
-- Original Message --
From: prem...@iiserpune.ac.in
To: gmxus...@gromacs.org
Greetings Gromacs Users,
I have run single precision isothermal-isobaric ensemble simulations using
particle mesh Ewald (PME) (in Gromacs 4.0.5) and compared the results to those
of (what I think should be) equivalent single precision simulations using the
classic implementation of Ewald. The
Hi all,
Is there a program that allows the user to add residues to the N and C
terminus, without using the electron density? I would like to add a
short linker to my protein which doesn't exist in the electron
density.
Thanks a lot,
Sincerely,
Zack
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gmx-users mailing list
Try Loopy. You can get it to build termini in addition to loops.
http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Loopy
Nevertheless, I'd suggest simply omitting that part of the protein and
capping your new terminus to remove the charge. You will have more
difficulties
On 6/20/11 Jun 20,1:01 PM, Gavin Melaugh wrote:
Hi all
I have read the manual and the recent JCTC paper on g_wham, and I was
wondering how to actually get the error bars on the profile.xvg file
outputted from g_wham.
Many Thanks
Gavin
Hi Gavin,
the error bars are at the moment only in
Hi,
Is it possible to get negative values for normalized autocorrelation of
total dipole moment.
Thank you.
Regards,
Chathurika.
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Please search the archive at
Any graphing program will do, the .xvg file is a text data file, so you can
import it into Excel, Sigma Plot, xmgrace, gnuplot etc.
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
Dear gromacs-ers
I am using stochastic dynamics integrator (integrator = sd), so most of the
time, I only need to adjust following parameters for temperature and
pressure coupling: tau_t pcoupl tau_p (ref_t is room temperature and ref_p
is 1 atm, compressibility can be taken from experimental
xiaodong huang wrote:
Dear gromacs-ers
I am using stochastic dynamics integrator (integrator = sd), so most of
the time, I only need to adjust following parameters for temperature and
pressure coupling: tau_t pcoupl tau_p (ref_t is room temperature and
ref_p is 1 atm, compressibility can
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