Hi Everyone,
I did another simulation where i found the the DPPC area per lipid is 0.61
nm^2 . Is this acceptable ?
I have seen issues like this on the mailing list before can one of the
experts give me some hints.
Amit
On Wed, Nov 9, 2011 at 12:24 PM, Amit Choubey kgp.a...@gmail.com wrote
5Hello all,
I am trying to use CHARMM 36 for DPPC membrane simulation. I did the
following so far:
1. Download pdb file containing 128 DPPC molecules from
http://www.charmm-gui.org/?doc=archivelib=lipid_pure
2. I separated one lipid molecule from the obtained pdb file and used
pdb2gmx -f
Use g_dist tool.
On Sun, Aug 28, 2011 at 8:38 AM, Sajad Ahrari sajadahr...@yahoo.com wrote:
Dear users,
is there any command in Gromacs to show fluctuations of distance, between
mass center for two groups of amino-acids in a protein, over time?
thanks,
sajad
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On Fri, Aug 19, 2011 at 8:50 AM, KONG Xian xiansh...@gmail.com wrote:
I have sent this email days ago, but I got no answer.
Hope someone would saw it this time.
Sorry for disturbing.
Dear all:
I am using gromacs-4.0.2_localpressure to calculate the local
On Fri, Aug 19, 2011 at 8:13 AM, Junior Nebeker junior.nebe...@gmail.comwrote:
Sure Mark. If your interest is in patrolling the Gromacs mailing list,
then I'll leave you to it.
I think before you type your response you should consider that Mark has
helped several hundred times over this
Justin, when i define the whole line charge as a charge group i do get a
coulomb energy contribution. I thought there would be no non-bonded
contribution. I use a very high cut-off (longer than chain length) and no
pbc. Am i missing something ?
On Sat, Aug 13, 2011 at 3:21 PM, Amit Choubey kgp.a
On Sun, Aug 14, 2011 at 1:23 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Amit Choubey wrote:
Justin, when i define the whole line charge as a charge group i do get a
coulomb energy contribution. I thought there would be no non-bonded
contribution. I use a very high cut-off (longer than chain
...@vt.edu wrote:
Amit Choubey wrote:
Following is the mdp file
cpp = /usr/bin/cpp
;define = -DFLEX_SPC
constraints = none
integrator = steep
nsteps = 1
;
; Energy minimizing stuff
;
emtol = 200
I change the maximum charge group size defined in the include/types/nblist.h
header from 32 to 267. Then grompp worked fine but the mdrun did not start.
The following error came out
Program mdrun_jptlc, VERSION 4.5.3
Source code file: ns.c, line: 2417
Fatal error:
Max #atoms in a charge group:
:43, Amit Choubey kgp.a...@gmail.com wrote:
The largest charge group contains 267 atoms. The maximum is 32.
Column 6 in the [atoms] section of the .top file defines the charge
group. If you want each atom to be in its own charge group, you can
set this to the same number as the atom number
I was not sure if changing the size of maxcg would not negatively influence
anything else. I will give it a try. Thanks Justin
On Sat, Aug 13, 2011 at 4:04 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Amit Choubey wrote:
I change the maximum charge group size defined in the
include/types
Hi all,
I am trying to do a calculation on an artificial line charge in vacuum. The
line charge has 267 atoms and each atom has a 1e charge. The atoms are
bonded by a bond term and an angle term. I defined the required itp files
and top file. When i issue
grompp_jpt -v -c parallel.gro -p
On Fri, Aug 12, 2011 at 8:55 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Amit Choubey wrote:
Hi all,
I am trying to do a calculation on an artificial line charge in vacuum.
The line charge has 267 atoms and each atom has a 1e charge. The atoms are
bonded by a bond term and an angle term
Hi,
reduced units works for LJ particles only. I am not sure if it works when
you include electrostatics. When you set charge = 1 it is 1electronic
charge. I would suggest not to use the reduced units for LJ in this
scenario.
Amit
On Fri, Jul 29, 2011 at 8:05 AM, Alex Marshall amars...@uwo.ca
still be a unit of length to
deal with.
Thanks,
Alex
On Fri, Jul 29, 2011 at 2:24 PM, Amit Choubey kgp.a...@gmail.com wrote:
Hi,
reduced units works for LJ particles only. I am not sure if it works when
you include electrostatics. When you set charge = 1 it is 1electronic
charge. I would
cannot make the comparison.
I guess I'm not actually using gmx.ff, I was just using the C6-C12
convention for LJ parameters used in that forcefield's ffnonbonded.itp.
On Fri, Jul 29, 2011 at 3:50 PM, Amit Choubey kgp.a...@gmail.com wrote:
I am not sure what you want to measure. You mentioned
this tpr file to v4.0.2_local_pressure to rerun the simulation.
Jianguo
--
*From:* Amit Choubey kgp.a...@gmail.com
*To:* Jianguo Li ljg...@yahoo.com.sg
*Cc:* Discussion list for GROMACS users gmx-users@gromacs.org
*Sent:* Thursday, 28 July 2011 09:27:04
*Subject
Hi all,
When i use the following
trjconv_without_shock -f all_molecules_500ns_fixedpbc.gro -o traj.gro -novel
-s npt.tpr
traj.gro still has velocities.
Amit
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done
On Thu, Jul 28, 2011 at 11:52 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Amit Choubey wrote:
Hi all,
When i use the following
trjconv_without_shock -f all_molecules_500ns_fixedpbc.**gro -o traj.gro
-novel -s npt.tpr
traj.gro still has velocities.
Please file an issue report
of conversion tpr files from v4.5 to v4.0 using CHARMM FF?
Thank you very much!
Cheers,
Jianguo
--
*From:* Amit Choubey kgp.a...@gmail.com
*To:* Jianguo Li ljg...@yahoo.com.sg
*Cc:* Discussion list for GROMACS users gmx-users@gromacs.org
*Sent:* Friday, 1 July
Hi all,
I am doing dppc-water simulation. I am using structure and topologies from
http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies
In version 4.0 when i do
grompp_v4.0.2 -v -c dppc128.pdb -o npt -f npt.mdp -p system.top
it creates npt.tpr without any errors.
Using the
Thanks Justin, I can see that there is no problem when i fix the
periodicity.
Amit
On Tue, Jul 19, 2011 at 2:52 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Amit Choubey wrote:
Hi all,
I am doing dppc-water simulation. I am using structure and topologies from
http
reruns were done
for two frames separately and a .trr which had these two frames only) and
the numbers did not seem to be averages.
Can someone help me in figuring out what is going on ?
Amit
On Tue, Jun 21, 2011 at 9:16 AM, Amit Choubey kgp.a...@gmail.com wrote:
On Tue, Jun 21, 2011 at 1:13
you use CHARMM FF in your simulations and how did you convert the
tpr files from v 4.5 to v 4.0?
Yes i have used CHARMM FF and i will have to figure out the conversion.
Cheers
Jianguo
--
*From:* Amit Choubey kgp.a...@gmail.com
*To:* Jianguo Li ljg...@yahoo.com.sg
in figuring out whats the issue ?
Thank You.
On Fri, Jun 17, 2011 at 6:00 PM, Amit Choubey kgp.a...@gmail.com wrote:
Dear all,
I installed the git version of local pressure calculation from
http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure
The I invoked mdrun
our whats going on ?
Amit Choubey
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*Sent:* Friday, 10 June 2011 07:10:35
*Subject:* Re: [gmx-users] local pressure calcuation for Gromacs-4.5
Amit Choubey wrote:
Thanks Justin, I tried to install the recent git version but the
configure file is missing. How should I install this version
Dear all,
I saw an unanswered post at
http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html
It is about calculating local pressure in v 4.5 when using CHARMM FF. Could
someone give me some pointers about this?
Thank you
Amit
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Thanks Justin, I tried to install the recent git version but the configure
file is missing. How should I install this version ?
On Thu, Jun 9, 2011 at 12:45 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Amit Choubey wrote:
Dear all,
I saw an unanswered post at
http://lists.gromacs.org
Well sometimes i run out of walltime when doing long simulations and append
helps me not to do any file management after restarting simulations from the
previous checkpoint.
On Fri, Jun 3, 2011 at 3:26 PM, Dimitar Pachov dpac...@brandeis.edu wrote:
At first, I thought the -append option of the
Hi ,
I wish to save velocities and coordinates every step for my system. For
saving disk space i dont want to save water molecules. How can i do this ?
Amit
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Can you provide more details ? Which graph are you talking about ?
Amit
On Mon, Jan 17, 2011 at 12:05 AM, bharat gupta bharat.85.m...@gmail.comwrote:
Hi all,
I am minimizing my protein (230 amino acids) with the minim.mdp file given
in the lysozyme tutorial but I am not getting a stable
OK what seemed wrong to you?
On Mon, Jan 17, 2011 at 12:24 AM, bharat gupta bharat.85.m...@gmail.comwrote:
I am doin the first minimization step.. here are the details of minim.mdp
file
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to
Check your log file to see if the minimization criterion was satisfied ie
the max force is less than emtol.
On Mon, Jan 17, 2011 at 12:29 AM, bharat gupta bharat.85.m...@gmail.comwrote:
The potential energy graph is not coming parallel to x-axis is getting down
towars the x-axis .. normally
Hi all,
I am trying to do pulling simulation. Following are the pull parameters
pull = umbrella
pull_geometry = direction
pull_vec1 = 0 0 1
pull_group1 = RNA
pull_rate1 = 0.01
pull_k1 = 1000
pull_start = yes
Everything works fine until the pull group COM reaches half the box length.
The COM
A. Lemkul jalem...@vt.edu wrote:
Amit Choubey wrote:
Hi all,
I am trying to do pulling simulation. Following are the pull parameters
pull = umbrella
pull_geometry = direction
pull_vec1 = 0 0 1
pull_group1 = RNA
pull_rate1 = 0.01
pull_k1 = 1000
pull_start = yes
Everything works fine
Hi,
I am still not able to see the reason for the periodic distances coming into
picture.
Also, why pull_geometry = direction_periodic cannot be used with P-coupling;
although it seems to do what i want.
Amit
On Mon, Jan 17, 2011 at 1:04 PM, Amit Choubey kgp.a...@gmail.com wrote:
Hi
(using pull_init1) should fix this issue but i am not confident.
Thanks for looking into this.
On Mon, Jan 17, 2011 at 5:36 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Amit Choubey wrote:
Hi,
I am still not able to see the reason for the periodic distances coming
into picture.
I guess I
It seems that i cannot figure out a way to change the absolute reference
point (Its the origin by default).
Amit
On Mon, Jan 17, 2011 at 5:52 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Amit Choubey wrote:
Yes Justin i understand that. Heres what i think is going on
I dont have any
try the -type option with dihedral
amit
On Fri, Jan 7, 2011 at 2:16 AM, Carla Jamous carlajam...@gmail.com wrote:
Hi Everyone,
Please I'm trying to calculate one dihedral angle as a function of time
during my simulation.
For this, I used g_angle. In the manual (version 4.0.3) it says: the
angle of a group of angles as a function of time!!
What does it mean?
Because I'm getting positive and negative values in the same plot. Are
these values the values of my dihedral angle as a function of time?
Thanks again,
Carla
On Fri, Jan 7, 2011 at 11:30 AM, Amit Choubey kgp.a
Make your box bigger?
2011/1/6 yuanyuan wang yilin3...@126.com
dear all,
I am doing a simulation that have many chains in a box , and I can
find a center for them after serval tries.
I use almost every option of trjconv,-pbc
mol,atom,res,whole,nojump , -ur compact, -center
There is something wrong with your initial configuration. May be you forgot
to take care of periodicity, how did you get your initial configuration?
Also notice that these kind of problems have been discussed previously.
Amit
On Tue, Jan 4, 2011 at 12:33 AM, mohsen ramezanpour
pass all of steps in UMbrella sampling tutorial with these
files,without any warning or error.
the one thing I changed is rotating box with editconf.
On Tue, Jan 4, 2011 at 12:38 PM, Amit Choubey kgp.a...@gmail.com wrote:
There is something wrong with your initial configuration. May be you
, Amit Choubey kgp.a...@gmail.com wrote:
May be you broke the molecule while using editconf. Try to fix the
periodicity by trjconv and then use it.
On Tue, Jan 4, 2011 at 1:14 AM, mohsen ramezanpour
ramezanpour.moh...@gmail.com wrote:
I generated my .top and .gro file as drug/enzyme
Your log file does indicate that the steepest descent converged. I dont know
why you have the error messages. Why not go ahead with MD ?
Amit
On Sun, Jan 2, 2011 at 10:35 PM, shikha agarwal shikhaiiit...@gmail.comwrote:
hi,
HAPPY NEW YEAR
I am experiencing a segmentation fault during mdrun
This may not be related but it was not straight forward to do DPPC membrane
simulation using CHARMM FF in gromacs. The DPPC molecule was not defined at
all in the FF files.
The DPPC is defined in terms of two more residues in CHARMM.
amit
On Thu, Dec 9, 2010 at 11:21 AM, Justin A. Lemkul
On Wed, Dec 8, 2010 at 4:01 AM, Sascha Hempel
sascha.hem...@bci.tu-dortmund.de wrote:
Hi all!
I am trying to add some hard spheres to my simulation. As far as i can
tell from the manual Gromacs supports only LJ or Buckingham for
non-bonded interaction.
Why cant you use LJ? By setting the
try using to find out, its described on
http://manual.gromacs.org/current/online/g_density.html
On Wed, Dec 8, 2010 at 4:10 AM, Morteza Khabiri khab...@greentech.czwrote:
Dear all
does somebody knows how -symm option from g_density command do the
calculations?
Or in other word what is the
results compared to the
old set.
Good luck.
On 5 December 2010 18:09, Amit Choubey kgp.a...@gmail.com wrote:
Hi all,
This is a question unrelated to gromacs but would pose it anyway to get
some hints from the experts.
I wish to set up DNA and DPPC lipid membrane simulation. Could someone
Hi all,
This is a question unrelated to gromacs but would pose it anyway to get some
hints from the experts.
I wish to set up DNA and DPPC lipid membrane simulation. Could someone
please refer to a relevant forcefield/tutorial for simulation of lipids with
DNA?
Any help will be really
Hi,
Define an itp file which has the non-bonded info. Then define a mdp (md
parameter file) and also make a structure file (gro). Also you need a
topology file (top) which corresponds to the structure file.
You will have to do some background work. Manual should be your friend.
amit
On Sat,
Hi all,
I was going through the very nicely presented tutorial by Justin (on KALP-15
in DPPC). I have one question regarding the non-bonded cut-offs. It seems
that people use many different values of non-bonded cut-off (varying from
0.9 nm to 1.2 nm or probably more). How should i choose the
:
On 21/11/2010 8:45 PM, Amit Choubey wrote:
Hi all,
I was going through the very nicely presented tutorial by Justin (on
KALP-15 in DPPC). I have one question regarding the non-bonded
cut-offs. It seems that people use many different values of non-bonded
cut-off (varying from 0.9 nm
but not impossible and it was already done
for TIP4P, see Kumar and Skinner, J. Phys. Chem. B, 112,8311-8318, 2008
I hope this help
Ivan
Amit Choubey wrote:
Hi all,
I was wondering if there is a way to define user defined potential which
involves 3 particles. Thank you for any input
Hi all,
I was wondering if there is a way to define user defined potential which
involves 3 particles. Thank you for any input.
Amit
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Hi Rossen,
Could you send me a documentation of memory usage by gromacs-4.5-beta1. I
would like to know the maximum no. of atoms that we can simulate on our
university supercomputer.
amit
On Fri, Jul 30, 2010 at 12:20 PM, Rossen Apostolov
rossen.aposto...@cbr.su.se wrote:
After months of
On Tue, May 25, 2010 at 2:32 PM, VANDANA KUMARI
kumar...@buckeyemail.osu.edu wrote:
Hello Gromacs Users,
I am trying to make tpr file for NPT equilibration after NVT equilibration
using
grompp -f npt.mdp -c nvt.gro -t nvt.trr -p topol.top -n index.ndx -o
npt.tpr
I am using parameter
On Tue, May 18, 2010 at 2:00 PM, Gaurav Goel gauravgoel...@gmail.comwrote:
Hello gmx-users users :)
I am modifying the 'g_msd' utility to be able to calculate viscosities
using the corresponding Einstein relationship according to equation
3.14 in Helfand E., Physical Review, 119, 1, 1960.
On Mon, May 17, 2010 at 6:45 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Amit Choubey wrote:
On Sun, May 16, 2010 at 7:41 PM, Justin A. Lemkul jalem...@vt.edumailto:
jalem...@vt.edu wrote:
Amit Choubey wrote:
On Sun, May 16, 2010 at 5:15 PM, Justin A. Lemkul
Hi Everyone,
I was doing MD with SPC waters and found something which i am not sure how
to explain.
I made a box of SPC water of dimension 4x4x4 nm^3 and filled with water
using grenbox .
I then did a nvt simulation at 300 K for 1 ns . I used berendsen coupling
and Reaction - Field for coulomb
Hi Justin,
Since the density (1 gm/cc) and T (300 K) correspond to ambient condition,
should not the equation of state dictate a pressure around 1 atm?
thank you
amit
On Sun, May 16, 2010 at 2:07 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Amit Choubey wrote:
Hi Everyone,
I was doing MD
On Sun, May 16, 2010 at 5:15 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Amit Choubey wrote:
Hi Justin,
Since the density (1 gm/cc) and T (300 K) correspond to ambient condition,
should not the equation of state dictate a pressure around 1 atm?
If the equation of state involves
On Sun, May 16, 2010 at 7:41 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Amit Choubey wrote:
On Sun, May 16, 2010 at 5:15 PM, Justin A. Lemkul jalem...@vt.edumailto:
jalem...@vt.edu wrote:
Amit Choubey wrote:
Hi Justin,
Since the density (1 gm/cc) and T (300 K
On Thu, Mar 25, 2010 at 9:49 PM, 程迪 chengdi123...@gmail.com wrote:
Hi, everyone
I have two simulations which could run well separately. Now I want to place
the box of simulation A onto the box of simulation B. What should I do to
realise that?
I've tried to copy and paste the .gro and .top
Hi,
If i remember correctly SPC/E water might be worth trying. There is plenty
of research paper in this field. Try this paper
http://pubs.acs.org/doi/abs/10.1021/jp003020w
Also P,T coupling have effects on Diffusion Coeff.
amit
On Fri, Mar 5, 2010 at 1:29 AM, Sunil Thapa mephy...@yahoo.com
) uname -a
mpi version mpirun --version or mpiexec --version
also compiler version that was used for compiling gromacs
On Четверг 04 марта 2010 03:15:53 Amit Choubey wrote:
Hi Roland,
I was using 32 nodes with 8 cores, each with 16 Gb memory. The system was
about 154 M particles. This should
(with the file)
Roland
On Wed, Mar 3, 2010 at 1:22 AM, Amit Choubey kgp.a...@gmail.com wrote:
Hi Roland
I tried 'which mdrun' but it only gives the path name of installation. Is
there any other way to know if the installation is 64 bit ot not?
Thank you,
Amit
On Tue, Mar 2, 2010
On Wed, Mar 3, 2010 at 7:34 AM, Roland Schulz rol...@utk.edu wrote:
Hi,
ok then it is compiled in 64bit.
You didn't say how many cores each node has and on how many nodes you want
to run.
Roland
On Wed, Mar 3, 2010 at 4:32 AM, Amit Choubey kgp.a...@gmail.com wrote:
Hi Roland,
It says
, 2010 at 3:56 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
- Original Message -
From: Amit Choubey kgp.a...@gmail.com
Date: Saturday, February 27, 2010 10:17
Subject: Re: [gmx-users] gromacs memory usage
To: Discussion list for GROMACS users gmx-users@gromacs.org
Hi Mark,
We have
Hi Mark,
Yes thats one way to go about it. But it would have been great if i could
get a rough estimation.
Thank you.
amit
On Tue, Mar 2, 2010 at 8:06 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 3/03/2010 12:53 PM, Amit Choubey wrote:
Hi Mark,
I quoted the memory usage
no other way than trying. But fortunately, the
memory requirements of a (very) long simulation are equal to that of a
very short one, so it doesn't need to cost much time.
Cheers,
Tsjerk
On Wed, Mar 3, 2010 at 5:31 AM, Amit Choubey kgp.a...@gmail.com wrote:
Hi Mark,
Yes thats one way
On Wed, Mar 3, 2010 at 12:48 AM, Amit Choubey kgp.a...@gmail.com wrote:
Hi Tsjerk,
I tried to do a test run based on the presentation. But there was a memory
related error (I had given a leverage of more than 2 GB).
I did not understand the 64 bit issue, could you let me know wheres
Hi,
I am having trouble with running gromacs with a large system. I am trying to
use several processors for the md. The error is a memory allocation error
and it might be due to low RAM or large no of particles. I want to know the
detailed memory usage of mdrun ie say for N atoms how much memory
Hi Lum,
These values have to be chosen very icarefully.
Many artifacts can show up due to poorly chosen cutoff. I would suggest to
get the parameters from a reproducible publication or something.
amit
On Fri, Feb 26, 2010 at 8:49 AM, Lum Nforbi lumngwe...@gmail.com wrote:
Hi all,
Please,
. Is this
true?
Thank you,
amit
On Fri, Feb 26, 2010 at 2:57 PM, Mark Abraham mark.abra...@anu.edu.auwrote:)
- Original Message -
From: Amit Choubey kgp.a...@gmail.com
Date: Friday, February 26, 2010 20:05
Subject: [gmx-users] gromacs memory usage
To: Discussion list for GROMACS users
Hi everyone,
I am afraid this is not really a gromacs related question. Could anyone
refer me to a review paper which discusses about simulating water? Does any
of them gives a comparative and complete study of molecular dynamics with
water , answering questions like which water model to use, how
you,
Amit Choubey
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Hi Everyone,
I am trying to run a simulation with the option pbc=xy turned on. I am
using 64 processors for the simulation. The mdrun_mpi evokes the following
error message before starting the md steps
There is no domain decomposition for 64 nodes that is compatible with the
given box and a
Hi Mark,
I am not using PME calculation.
I was hoping mdrun will do the cell allocation itself.
Thanks,
Amit
On Fri, Feb 19, 2010 at 2:27 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
- Original Message -
From: Amit Choubey kgp.a...@gmail.com
Date: Saturday, February 20, 2010 8
Hi Mark,
I dont think i need to play with npme at all.
Amit
On Fri, Feb 19, 2010 at 2:41 PM, Amit Choubey kgp.a...@gmail.com wrote:
Hi Mark,
I am not using PME calculation.
I was hoping mdrun will do the cell allocation itself.
Thanks,
Amit
On Fri, Feb 19, 2010 at 2:27 PM, Mark
= 0
QMMMscheme = 0
scalefactor = 1
qm_opts:
ngQM = 0
On Fri, Feb 19, 2010 at 3:46 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
- Original Message -
From: Amit Choubey kgp.a...@gmail.com
Date: Saturday, February 20, 2010 10:25
Hi Everyone,
I changed the gromacs source code a little bit and this change introduced
some bias along x direction. Now i want to do a 'yz' pbc but gromacs has the
option of pbc = xy only. Is there a quick tip to circumvent? I can always
introduce the bias along z but its a little time taking job
Hi Everyone,
I have been trying to calculate diffusion coefficient for water. I am trying
to reproduce the numbers published in journal papers.
I am using SPCE water model. I use the g_msd analysis tool.
g_msd -f traj.trr -n index.ndx -s npt.tpr -b 2 -e 8
I use a box of volume 6x6x6 nm^3 which
, Mark Abraham mark.abra...@anu.edu.auwrote:
Amit Choubey wrote:
Hi Mark,
Ok here is the command line i used :-
g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e 804 -all
output is
# This file was created Tue Dec 1 20:20:41 2009
# by the following command:
# g_angle -f
On Wed, Dec 2, 2009 at 12:07 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Amit Choubey wrote:
Hi Mark,
That is true. But what does the manual refer to when it says
the first graph is the average, the rest are the individual angles
what and where are the rest? I am only curious because
Hi Justin,
Yes I understand what you are saying.
Thank you
amit
On Wed, Dec 2, 2009 at 12:50 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Amit Choubey wrote:
On Wed, Dec 2, 2009 at 12:07 PM, Justin A. Lemkul jalem...@vt.edumailto:
jalem...@vt.edu wrote:
Amit Choubey wrote
Hi everyone,
I am trying to analyze dihedrals of molecules after a simulation. I am able
to calculate dihedral distribution at ant particular time using g
-angle and proper group using
g_angle -f after_md.trr -b 800 -type dihedral -n chain1.ndx -od dihed12
This gives me the distribution at
explicitly by doing few more g_angle commands and it
seems that -all does do what i wanted to do. I still dont know what the
rest are the individual angles means.
Thank you,
Amit
On Tue, Dec 1, 2009 at 6:52 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
Amit Choubey wrote:
Hi everyone,
I am
= 800ps and 802 ps snapshots. I
checked this part.
Amit
On Tue, Dec 1, 2009 at 8:15 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
Amit Choubey wrote:
Hi Mark,
It does seem that the -all option averages the distributions. The thing is
i was confused with the first graph is the average
Hi everyone,
I was looking at calculation od dihedrals using g_angle. I did not
understand what the output of this tool is, along the x-axis we have angle
(in degrees) but what do we have along the y axis . Does y-axis show the
fraction of dihedrals having that specific angle? It does seem so by
On Wed, Nov 18, 2009 at 9:29 PM, sukesh chandra gain suk...@atc.tcs.comwrote:
Dear All,
I started a protein simulation for 100ps with octahedron box. After
completion of that run I visualized the protein at the centre of the
octahedron box by using trjconv.
Then I have extended the
you could try to write your top files in the working directory and use
pdb2gmx -ff option. By default, gromacs first searches in the working
directory.
amit
On Sat, Nov 14, 2009 at 9:05 AM, Jiang Zhu zhujiang2...@gmail.com wrote:
Dear all,
I have been a GROMACS user for some time but
hi,
could you specify the system size?
How many steps did it run before you got the segmentation fault? Try to find
if everything went ok until the segmentation fault by saving log and
trajectories.
amit
On Fri, Nov 13, 2009 at 3:53 PM, Justin A. Lemkul jalem...@vt.edu wrote:
in your previous run you might be saving the trajectory in some other *.trr
file . Try appending in that.
amit
On Fri, Nov 13, 2009 at 9:11 AM, Yi Peng muhuohuo...@gmail.com wrote:
Hi, everyone,
I was using Gromacs-4.0.3 to run my MD calculations parallell on our High
performance clusters
On Tue, Nov 10, 2009 at 4:32 AM, Marcovitz Amir amarcov...@gmail.comwrote:
Hi Amit,
Unfortunately, i don't have an answer to your question as i am a very
new GROMACS user myself..
Actually i might need your help.
I need to model two charged plates with opposite signs which are
solvated
Hi everyone,
I want to do an exact continuation with saved configuration and velocity.
What are the options that i need to change in mdp file?
I know i have to make unconstrained_start = yes. Anything else?
The reason i am asking this is that it is kind of difficult to make sure if
i am doing
On Tue, Nov 10, 2009 at 6:11 PM, Jack Shultz
j...@drugdiscoveryathome.comwrote:
Hi I am trying to generate xvg files for my simulation. Which
parameter do I need to specify?
xvg files for what? They are used for data files for 2D plots of quantities
that can be analyzed...
Can you be more
' and then analyze the
trajectory (.xtc) and energy (.edr) files generated. It takes quite some
time to figure out the first step 'mdrun' :)
amit
On Tue, Nov 10, 2009 at 9:24 PM, Amit Choubey kgp.a...@gmail.com wrote:
On Tue, Nov 10, 2009 at 6:11 PM, Jack Shultz j
is for writing xtc file
http://manual.gromacs.org/current/online/mdrun.html should help
On Tue, Nov 10, 2009 at 9:43 PM, Amit Choubey kgp.a...@gmail.com wrote:
On Tue, Nov 10, 2009 at 6:31 PM, Jack Shultz j...@drugdiscoveryathome.com
wrote:
Actually I guess I need to generate the xtc
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