Hi Users,
I did the following step=
pdb2gmx -ignh -f 1ahw.pdb -o sample.pdb -p sample.top
and received an error= Atom ND1 not found in residue seq.nr. 7 while adding
atom.
I dont understand how do i rectify this.
--
Aiswarya
--
gmx-users mailing listgmx-users@gromacs.org
an external tool to process your PDB file adding
the missing atoms. I've used SwissPDB and worked fine.
Javier
El 18/04/12 11:24, aiswarya pawar escribió:
Hi Users,
I did the following step=
pdb2gmx -ignh -f 1ahw.pdb -o sample.pdb -p sample.top
and received an error= Atom ND1 not found
at 12:41 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 29/02/2012 6:01 PM, aiswarya pawar wrote:
Mark,
Right now am computing distance between each protein atom against all
water atoms,
That's expensive. mdrun goes to great lengths to speed up computing
billions of distances.
which
:12 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 29/02/2012 7:21 PM, aiswarya pawar wrote:
Mark,
i want to know which water atoms stay within a cut off to protein atom.
OK, but as you will read in g_mindist -h, it will count such atoms and not
identify which they were...
ie i need
Dear all,
Am running g_mindist on large number of atoms, i would like to know whether
i can run this on more than one processors say 8 processors to speed up the
task? and will this effect the output in anyways.
Thanks,
--
Aiswarya B Pawar
--
gmx-users mailing listgmx-users@gromacs.org
:
On 29/02/2012 5:17 PM, aiswarya pawar wrote:
Dear all,
Am running g_mindist on large number of atoms, i would like to know
whether i can run this on more than one processors say 8 processors to
speed up the task?
No. If it will take too long, you need to reduce your number of frames
Dear Gromacs users,
I have a MD simulated protein and i take frame from this and remove water
and add water implicit in the interface and want to do energy minimization
but while doing the minimization i get errors. The steps followed are-
pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top
Dear Gromacs users,
I have a MD simulated protein and i take frame from this and remove water
and add water implicit in the interface and want to do energy minimization
but while doing the minimization i get errors. The steps followed are-
pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top
By setting the emtol to 1.0, didnt work. Anyother way i could figure out.
On Thu, Feb 9, 2012 at 6:32 PM, Justin A. Lemkul jalem...@vt.edu wrote:
lina wrote:
On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar aiswarya.pa...@gmail.com
wrote:
Dear Gromacs users,
I have a MD simulated protein
Dear Gromacs Users,
i have data for the distance between the protein and water atoms within a
cut off of 8A for 5ns using the g_dist option. Now i want to use g_analyze
on this data. The time frame in the output data is not continuous because
of the cut off provided. So i would like to know how
at 6:48 PM, Justin A. Lemkul jalem...@vt.edu wrote:
aiswarya pawar wrote:
Dear Gromacs Users,
i have data for the distance between the protein and water atoms within a
cut off of 8A for 5ns using the g_dist option. Now i want to use g_analyze
on this data. The time frame in the output data
the protein water distance within 0.8nm are shown. So is it
possible to do g_analyze on this?
On 01-Feb-2012, at 6:48 PM, Justin A. Lemkul wrote:
aiswarya pawar wrote:
Dear Gromacs Users,
i have data for the distance between the protein and water atoms within a
cut off of 8A for 5ns using
On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham mark.abra...@anu.edu.au
wrote:
On 19/01/2012 8:45 PM, aiswarya pawar wrote:
Mark,
THe normal mdrun also hangs thus not generating any output.
OK. It's your problem to solve... keep simplifying stuff until you can
isolate a small number
when i tired running it again, i got an error as
Cuda error in file
'/home/staff/sec/secdpal/software/openmm_tesla/platforms/cuda/./src/kernels//
bbsort.cu' in line 176 : unspecified launch failure.
/bin/cat: file_loc: No such file or directory
On Thu, Jan 19, 2012 at 8:45 PM, aiswarya pawar
can mean anything,
from faulty hardware to bad driver to messed up installation.
Does the memory test run? Try to compile/install again and see if it works.
--
Szilárd
On Thu, Jan 19, 2012 at 4:18 PM, aiswarya pawar
aiswarya.pa...@gmail.com wrote:
when i tired running it again, i got
: No such file or directory
On Thu, Jan 19, 2012 at 11:41 PM, Justin A. Lemkul jalem...@vt.edu wrote:
aiswarya pawar wrote:
Szilárd,
I did a memory test run yesterday and it went fine but today received an
error. So you mean to say the tesla card version nothing to do with this
right.
You're
Hi users,
Am running mdrun on gpu . I receive an error such as=
WARNING: This run will generate roughly 38570 Mb of data
WARNING: OpenMM does not support leap-frog, will use velocity-verlet
integrator.
WARNING: OpenMM supports only Andersen thermostat with the
md/md-vv/md-vv-avek
error
Hi,
Most of those are just warnings, the only error I see there comes from
the shell, probably an error in your script.
Cheers,
--
Szilárd
On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar
aiswarya.pa...@gmail.com wrote:
Hi users,
Am running mdrun on gpu . I receive an error
Hi users,
Am trying to run the grimaces gpu version. I receive an error while doing
the nvt step . my nvt.mdp file goes like this=
; VARIOUS PREPROCESSING OPTIONS
title= NVT simulation (constant number, volume and
temperature)
cpp = /lib/cpp
; RUN
Yes it worked. Thanks :)
On Tue, Jan 17, 2012 at 10:26 PM, Justin A. Lemkul jalem...@vt.edu wrote:
aiswarya pawar wrote:
Hi users,
Am trying to run the grimaces gpu version. I receive an error while doing
the nvt step . my nvt.mdp file goes like this=
; VARIOUS PREPROCESSING OPTIONS
You can write this on VMD forum. Anyways you can try by doing this in the
Tcl console-
set sel [atomselect top solvent]
$sel get {x y z}
This would give you the coordinates of the solvent, for your purpose you
got to iterate so as to get for each time step.
Aiswarya
SERC Dept, IISc
Bangalore
Dear Users,
Am running a shell script for the command g_mindist=
#!/bin/bash
groups=`grep ^\[ -o index.ndx | wc -l`
for ((i=0; i$groups; i++))
do
echo $((i++)) 3393 | g_mindist -f md.xtc -s md.tpr -od $i.xvg -o
atm-pair$i.out -d 0.8 -e 5000 -n index.ndx
done
here the index file has 3393
I did few changes ie decreased the time step/ increased the equilibration
steps/ omitted the generation of velocity in production run / did 2 steps of
equilibration / checked the starting structure for steric clashes.
I don't understand what else should I try to fix the lincs warnings.
Sent
. Is anything wrong with my
protein.
On Sun, Dec 18, 2011 at 7:35 PM, aiswarya pawar aiswarya.pa...@gmail.comwrote:
Hi users,
I did energy minimization of a protein complex using the following
minimization mdp file.
; Lines starting with ';' ARE COMMENTS
; Everything following ';' is also comment
rectify this. Please help
On Sun, Dec 18, 2011 at 8:12 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 19/12/2011 1:05 AM, aiswarya pawar wrote:
Hi users,
I did energy minimization of a protein complex using the following
minimization mdp file.
See
http://www.gromacs.org/Documentation
Hi users,
I did energy minimization of a protein complex using the following
minimization mdp file.
; Lines starting with ';' ARE COMMENTS
; Everything following ';' is also comment
title = Energy Minimization ; Title of run
; The following line tell the program the standard locations where to
/2011 4:55 PM, aiswarya pawar wrote:
Hi users,
i would like to know which version of gromacs would be compatible with
the cluster architecture =
Linux cnode39 2.6.5-7.244-pseries64 #1 SMP Mon Dec 12 18:32:25 UTC 2005
ppc64 ppc64 ppc64 GNU/Linux
Any.
And which gromacs version would
Lina,
I used the same script for mpi ie other than usr/bin/poe I have given
usr/bin/mpirun I still receive the same errorOn 15/12/2011 4:51 PM, aiswarya pawar wrote:
Hi,
When i tried running mdrun without mip i received the same error ie
when i gave mdrun -deffnm md
i got=
Back Off! I
Hi users,
i would like to know which version of gromacs would be compatible with the
cluster architecture =
Linux cnode39 2.6.5-7.244-pseries64 #1 SMP Mon Dec 12 18:32:25 UTC 2005
ppc64 ppc64 ppc64 GNU/Linux
And which gromacs version would be compatible with the mpi version =
mpich-1.2.7
Hi users,
I have a submission script for gromacs mdrun to be used on IBM cluster, but
i get an error while running it. the script goes like this=
#!/bin/sh
# @ error = job1.$(Host).$(Cluster).$(Process).err
# @ output = job1.$(Host).$(Cluster).$(Process).out
# @ class = ptask32
# @ job_type =
usersgmx-users@gromacs.org
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
Subject: Re: [gmx-users] submission error
On 14/12/2011 10:30 PM, aiswarya pawar wrote:
Hi users,
I have a submission script for gromacs mdrun to be used on IBM
cluster, but i get an error while running
To: Discussion list for GROMACS usersgmx-users@gromacs.org
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
Subject: Re: [gmx-users] submission error
On 14/12/2011 10:30 PM, aiswarya pawar wrote:
Hi users,
I have a submission script for gromacs mdrun to be used on IBM
cluster
Thanks,
Aiswarya
On Wed, Dec 14, 2011 at 5:00 PM, aiswarya pawar aiswarya.pa...@gmail.comwrote:
Hi users,
I have a submission script for gromacs mdrun to be used on IBM cluster,
but i get an error while running it. the script goes like this=
#!/bin/sh
# @ error = job1.$(Host).$(Cluster
Hi gromacs users,
Iam trying to install gromacs on IBM cluster. I have successfully installed
installed fftw-3.3 version with commands=
./configure --enable-threads --enable-float
make
make install
the set the enviroment=
setenv CPPFLAGS -I/home/fftw/include
setenv LDFLAGS -L/home/fftw/lib
]: *** [libgmxpreprocess_mpi.la] Error 1
make[1]: Leaving directory
`/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/kernel'
make: warning: Clock skew detected. Your build may be incomplete.
On Sat, Dec 10, 2011 at 1:05 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 10/12/2011 6:31 PM, aiswarya pawar wrote
On Thu, Dec 8, 2011 at 5:32 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 8/12/2011 6:35 PM, aiswarya pawar wrote:
Hi users,
Am running the mdrun_mpi on cluster with the md.mdp parameters as-
; VARIOUS PREPROCESSING OPTIONS
title= Position Restrained Molecular Dynamics
, aiswarya pawar aiswarya.pa...@gmail.comwrote:
Hi,
I tried giving this-
./configure --prefix=/home/soft/gromacs --host=ppc --build=ppc64
--enable-mpi --with-fft=fftw3 MPICC=mpcc CC=xlc CFLAGS=-O3 -qarch=450d
-qtune=450 CXX=mpixlC_r CXXFLAGS=-O3 -qarch=450d -qtune=450
and the configure process
when i gave following command for gromacs=
./configure --with-fft=fftw3 --enable-float --disable-threads
it installed gromacs successfully, but i require a mpi mdrun. when i give
enable mpi it gives me same error as fftw3 library not found.
Thanks
On Wed, Dec 7, 2011 at 2:21 PM, Javier
Hi users,
Am running the mdrun_mpi on cluster with the md.mdp parameters as-
; VARIOUS PREPROCESSING OPTIONS
title= Position Restrained Molecular Dynamics
; RUN CONTROL PARAMETERS
constraints = all-bonds
integrator = md
dt = 0.002 ; 2fs !
nsteps = 250 ; total 5000 ps.
Hi Gromacs users,
Am trying to install gromacs-4.5.5 version on IBM cluster with Linux
platform and am getting an error such as configure: error: Cannot find
fftw3f library.
The steps i followed-
Installed fftw-3.3 version
./configure --enable-threads --enable-float
make
make install
setenv
Hi,
Thanks for the reply, I check the path and everything still I get this error.
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
-Original Message-
From: Javier Cerezo j...@um.es
Sender: gmx-users-boun...@gromacs.org
Date: Tue, 06 Dec 2011 13:30:55
To:
Hi users,
Iam running a minimization on protein complex in vacuum. i have set the
parameters as following-
; Lines starting with ';' ARE COMMENTS
; Everything following ';' is also comment
title= Energy Minimization; Title of run
; The following line tell the program the standard
is it saying that Timesteps at t=31 don't match (12, 26).
On Fri, Oct 21, 2011 at 12:25 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 21/10/2011 5:09 PM, aiswarya pawar wrote:
Hi users,
Iam running a minimization on protein complex in vacuum. i have set the
parameters as following-
; Lines
Hi Users,
I performed a simple minimization for a protein complex in vacuum. Didn't get
any error while performing the minimization but when visualised the pdb file
after the minimization the chains of the protein complex separated.
What could be the reason.
Thanks,
Aiswarya
Sent from my
Hi,
All the parameters are ok, still i get the complex separated.
On Wed, Oct 19, 2011 at 7:02 PM, Justin A. Lemkul jalem...@vt.edu wrote:
aiswarya.pa...@gmail.com wrote:
Hi Users,
I performed a simple minimization for a protein complex in vacuum. Didn't
get any error while performing
Hi users,
I have n number of program to run so my index file is huge, i want to know
if i use the command option g_energy -flags choice.txt , it takes up the
numbers given right? but if i have n numbers in the choice txt. how would it
take in each run , ie it will take 1st two numbers and what
justin,
if i use echo command then i need to run again and again for each selection
right? how can i run as whole bunch.
Thanks
On Wed, Sep 28, 2011 at 10:31 PM, Justin A. Lemkul jalem...@vt.edu wrote:
aiswarya pawar wrote:
Hi users,
I have n number of program to run so my index file
:
aiswarya pawar wrote:
justin,
if i use echo command then i need to run again and again for each
selection right? how can i run as whole bunch.
I don't understand your question. You can write a trivial shell script for
all of your analysis, e.g.:
#!/bin/bash
echo 4 4 | g_rms -f traj.xtc -s
Hi users,
I have data with the time frame and the distances, how will compute the
autocorrelation of this. i did g_analyze but still dont understand what
should be the y axis data when providing input for g_analyze. please help.
Thanks
--
gmx-users mailing listgmx-users@gromacs.org
, Sep 26, 2011 at 12:38 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 26/09/2011 4:51 PM, aiswarya pawar wrote:
Hi users,
I have data with the time frame and the distances, how will compute the
autocorrelation of this. i did g_analyze but still dont understand what
should be the y axis
Mark,
i read the help but i still didnt understand how do i compute the time
series for this data, should i use this data as such for the input?
Thanks,
On Mon, Sep 26, 2011 at 12:44 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 26/09/2011 5:10 PM, aiswarya pawar wrote:
HI Mark,
i
Hi users,
I have got a data from g_mindist ie water and protein atom distance in each
time frame. Now I have to find the auto correlation function using g_analyze
but my output file from g_mindist has the time frame,water molecule number. How
do I compute the ACF. In ACF data set the x axis is
Hi users,
The g_mindist gives the minimum distance between the atoms other than the
actual distance.
Thanks
--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search
, what did you get, what did you expect and what is
your hunch regarding the difference between your result and your
expectation?
Tsjerk
On Thu, Sep 22, 2011 at 8:21 AM, aiswarya pawar
aiswarya.pa...@gmail.com wrote:
Hi users,
The g_mindist gives the minimum distance between the atoms
Hi users,
what are options for obtaining the surface atoms exposed to solvent, i need
the list of these atoms.
Thanks
--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
Hi users,
Am using g_mindist to calculate the distances. Now I have to calculate for each
atom ie around 1000atoms. If I try running this command in a shell script, how
would designate the index file, ie my index file has protein atoms and water
atoms, and have to find distance between one
Hi Users,
When i list the residues in a index file it shows a numbering of residues
and when open the same protein in VMD and check the residue numbering its
different. i want to visualise the protein in VMD and select a residue
number from VMD and use in gromacs ie want to make an index file in
as-
t:1 1322 a 54119 OW 0.389
but am getting something different
On Tue, Sep 13, 2011 at 11:24 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 13/09/2011 3:40 PM, aiswarya pawar wrote:
Hi Mark,
The -dist option says- print all the atoms in group 2 that are closer than
a certain
g_dist -f md.xtc -s md.tpr -dist 0.5 -e 500 if the index name not given it
takes the default index file, so there isnt any wrong in selecting the
atoms.
On Tue, Sep 13, 2011 at 1:24 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 13/09/2011 4:14 PM, aiswarya pawar wrote:
Mark
Hi everyone,
when am doing this g_dist between the protein and water am getting the
distance between water-water. why it is so?? and is there a way i can find
distance in each time frame.
Thanks
On Thu, Sep 8, 2011 at 5:55 PM, aiswarya pawar aiswarya.pa...@gmail.comwrote:
Hi users,
To get
Hi Users,
Am using g_dist to find the distance between water and protein. but my
output has the values of SOL-water distance.
t: 1 136 SOL 2336 OW 0.772373 (nm)
Thanks
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Please search the
Hi gromacs Users,
Am using g_dist to find the distance between water and protein. for
that i made a index file such as-
a CA(protein atoms)
a OW(water atoms)
i then run this cmd- g_dist -f md.xtc -s md.tpr -n index.ndx -e 500 -dist 0.35
instead of getting the result for protein-SOL distance .
output
shows SOL-OW distance as seen below-
t: 1 136 SOL 2336 OW 0.772373 (nm)
even after specifying am getting an wrong output.
Thanks
On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul jalem...@vt.edu wrote:
aiswarya pawar wrote:
Hi Users,
Am using g_dist to find the distance between
hi Justin,
As far i referred the OW,HW1 etc are water atoms so how can it be distance
between the SOL protein atoms, instead it is SOL water atoms.
Thanks
On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul jalem...@vt.edu wrote:
aiswarya pawar wrote:
Hi Users,
Am using g_dist to find
hi Justin,
As far i referred the OW,HW1 etc are water atoms so how can it be distance
between the SOL protein atoms, instead it is SOL water atoms.
Thanks
On Mon, Sep 12, 2011 at 4:53 PM, Justin A. Lemkul jalem...@vt.edu wrote:
aiswarya pawar wrote:
Hi gromacs Users,
Am using g_dist
gmx-users@gromacs.org
Subject: Re: [gmx-users] g_dist error
aiswarya pawar wrote:
hi Justin,
As far i referred the OW,HW1 etc are water atoms so how can it be
distance between the SOL protein atoms, instead it is SOL water atoms.
The printed distance indicates that there is a certain water
...@gromacs.org
Date: Mon, 12 Sep 2011 07:52:54
To: Discussion list for GROMACS usersgmx-users@gromacs.org
Reply-To: jalem...@vt.edu,
Discussion list for GROMACS users gmx-users@gromacs.org
Subject: Re: [gmx-users] g_dist error
aiswarya pawar wrote:
hi Justin,
As far i referred the OW
...@vt.edu,
Discussion list for GROMACS users gmx-users@gromacs.org
gmx-users@gromacs.org
Subject: Re: [gmx-users] g_dist error
aiswarya pawar wrote:
hi Justin,
As far i referred the OW,HW1 etc are water atoms so how can it be
distance between the SOL protein atoms, instead
Hi all,
am facing an error while installing gridcount-
make[1]: *** [g_ri3Dc.o] Error 1
make[1]: Leaving directory `/home/proj11/aiswarya/Grid-count/src'
make: *** [all] Error 2
This error is while giving the make command.
Thanks
--
gmx-users mailing listgmx-users@gromacs.org
Hi gromacs users,
Is there a way to convert gromacs topology format to Amber.
Thanks,
Aiswarya
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Please search the archive at
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Hi users,
To get the distance between water and protein i did -
g_dist -f md.xtc -s md.tpr -o distance.xvg -dist 1 -b 1 -e 11
from this i should obtain an output file as distance.xvg which i dont get.
and my output is printed on the terminal as-
t: 1 136 SOL 2336 OW 0.772373 (nm)
t: 1 136
Thanks Lina and Justin.
Is this data good for finding the distance of protein and water as function
of time.
On Thu, Sep 8, 2011 at 5:55 PM, aiswarya pawar aiswarya.pa...@gmail.comwrote:
Hi users,
To get the distance between water and protein i did -
g_dist -f md.xtc -s md.tpr -o
Hi Gromacs users,
Am running a MD simulation over a protein complex and before adding the
ions. we run a grompp option then we get result as model net charge as some
integer ie if +2.00. so we got to add 2 CL ions. But when i ran my protein
for grompp it didnt give me any net charge so am not
--Original Message--
From: Mark Abraham
To: Aiswarya Pawar
Subject: Re: [gmx-users] Hydrogen existence time
Sent: 24 Aug 2011 6:09 PM
On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote:
Any idea how can I calculate the residence time of water.
First, seek define what you mean
of 1 when x=y(x not equal to 0 and y
not equal to 0) ie the site occupied and when x not equal to y or both x and
y =0. N(t) index of water molecule found in the hydration site at time t.
Aiswarya
--Original Message--
From: Mark Abraham
To: Aiswarya Pawar
Subject: Re: [gmx-users
Hello Everyone,
Any idea how one can convert gromacs trajectory file to amber file. So as to
use the amber tools.
Thank you,
Aiswarya
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gmx-users mailing listgmx-users@gromacs.org
Hi Justin,
Thank for the quick response. I would try out your script for the conversion.
Best,
Aiswarya
--Original Message--
From: Justin A. Lemkul
To: Aiswarya Pawar
To: Discussion list for GROMACS users
ReplyTo: jalem...@vt.edu
Subject: Re: [gmx-users] Conversion of gromacs trajectory
Dear all,
Does Hydrogen bond existence in a time frame states the residence time of the
water molecule?
Thank you,
Aiswarya
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gmx-users mailing listgmx-users@gromacs.org
Dear Justin,
So what does the hydrogen bond existence state?
Thanks
--Original Message--
From: Justin A. Lemkul
To: Aiswarya Pawar
To: Gromacs mail
ReplyTo: jalem...@vt.edu
Subject: Re: [gmx-users] Hydrogen existence time
Sent: 24 Aug 2011 5:54 PM
aiswarya.pa...@gmail.com wrote:
Dear
Any idea how can I calculate the residence time of water.
Aiswarya
--Original Message--
From: Justin A. Lemkul
To: Aiswarya Pawar
To: Gromacs mail
ReplyTo: jalem...@vt.edu
Subject: Re: [gmx-users] Hydrogen existence time
Sent: 24 Aug 2011 5:58 PM
aiswarya.pa...@gmail.com wrote:
Dear
Dear Emanuel,
Iam following what you have mentioned earlier. But as you said hydrogen bond
correlation time gives the average hydrogen bond existence time. So I confused
understanding whether an H Bond existence time would give me the residence time.
Aiswarya
Sent from my BlackBerry® on
site at time t.
Aiswarya
--Original Message--
From: Mark Abraham
To: Aiswarya Pawar
Subject: Re: [gmx-users] Hydrogen existence time
Sent: 24 Aug 2011 6:09 PM
On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote:
Any idea how can I calculate the residence time of water.
First, seek
of water molecule found in the hydration site at time t.
Aiswarya
--Original Message--
From: Mark Abraham
To: Aiswarya Pawar
Subject: Re: [gmx-users] Hydrogen existence time
Sent: 24 Aug 2011 6:09 PM
On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote:
Any idea how can I calculate
.
Aiswarya
--Original Message--
From: Mark Abraham
To: Aiswarya Pawar
Subject: Re: [gmx-users] Hydrogen existence time
Sent: 24 Aug 2011 6:09 PM
On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote:
Any idea how can I calculate the residence time of water.
First, seek define what you mean
Mark,
Sorry for the trouble.
Aiswarya
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
-Original Message-
From: Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de
Sender: gmx-users-boun...@gromacs.org
Date: Mon, 22 Aug 2011 12:36:02
To:
Dear Emanuel,
Thank you so much for the response.
I did the H bond count using the g_hbond. After this these H bond are
correlated against time right?? I just want to make sure I got it right. And
more over I should give a distance constrain so as to give me the existence of
water at a time.
Hi,
I have simulated a protein complex and now i would like to know the residing
water molecules between the protein complex. g_hbond and trjorder helps in
giving the number of hydrogen bonds and distance. but is this the residence
time calculation. please help me with this. there few posts given
Hi,
I have simulated a protein complex and now i would like to know the residing
water molecules between the protein complex. g_hbond and trjorder helps in
giving the number of hydrogen bonds and distance. but is this the residence
time calculation. please help me with this. there few posts given
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