u can use 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 s
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
http://lists.g
:12 PM, Mark Abraham wrote:
> 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 w
12:41 PM, Mark Abraham wrote:
> 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
2 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 nu
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
ht
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 wrote:
>
>
> lina wrote:
>
>> On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar
>> wrote:
>>
>>> Dear Gromacs users,
>>>
&g
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 -nocmap
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 -nocmap
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
>
012 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 the g_dist option. Now i want to use g_analyze
>> on
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 wo
Hi Users,
Is it possible to run gromacs executables solely on GPU (nvidia with cuda
libraries) without using CPU. Where can I get more information about this.
Thank you,
Aiswarya
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!--
gmx-users mailing listgmx-user
t: file_loc: No such file or directory
On Thu, Jan 19, 2012 at 11:41 PM, Justin A. Lemkul 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
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
> wrote:
> > when i tired running it
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, aisw
gt;
>
>
> On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham
> 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 t
eply-To: Discussion list for GROMACS users
>
> Subject: Re: [gmx-users] mdrun-gpu 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
>
>
>
&
ly 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
wrote:
> Hi users,
>
> Am running mdrun on gpu . I receive an error such as=
>
> WARNING: This run will generate roughly 38570 Mb of d
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 integrators.
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
Yes it worked. Thanks :)
On Tue, Jan 17, 2012 at 10:26 PM, Justin A. Lemkul 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=
&
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 CONTROL
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 33
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 f
anything wrong with my
protein.
On Sun, Dec 18, 2011 at 7:35 PM, aiswarya pawar wrote:
> Hi users,
>
> I did energy minimization of a protein complex using the following
> minimization mdp file.
>
> ; Lines starting with ';' ARE COMMENTS
> ; Everything followin
rectify this. Please help
On Sun, Dec 18, 2011 at 8:12 PM, Mark Abraham wrote:
> 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.gro
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
I did the openmpi installation on IBM cluster, when i try to run the md.tpr
is read but gets abort and leaves and error saying=
p4_error: interrupt SIGx:4
Anyone knows the solution to this.
Thanks,
Aiswarya
On Fri, Dec 16, 2011 at 2:28 PM, Mark Abraham wrote:
> On 16/12/2011 4:55 PM, aiswa
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
Thank
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
Thanks,
Aiswarya
On Wed, Dec 14, 2011 at 5:00 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 it. the script goes like this=
>
> #!/bin/sh
> # @ error = job1.$(Host).$(Cl
s
Reply-To: Discussion list for GROMACS users
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 it. the script goes li
ssion list for GROMACS users
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 it. the script goes like this=
>
>
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 =
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
The
ent `../mdlib/libmd_mpi.la'
make[1]: *** [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 wrote:
>
r unhandled
argument `../mdlib/libmd_mpi.la'
make[1]: *** [libgmxpreprocess_mpi.la] Error 1
On Sat, Dec 10, 2011 at 1:01 PM, aiswarya pawar wrote:
> Hi,
>
> I tried giving this-
>
>
> ./configure --prefix=/home/soft/gromacs --host=ppc --build=ppc64
> --enable-mpi
ary `../mdlib/libmd_mpi.la' or unhandled
argument `../mdlib/libmd_mpi.la'
make[1]: *** [libgmxpreprocess_mpi.la] Error 1
On Thu, Dec 8, 2011 at 5:32 PM, Mark Abraham wrote:
> On 8/12/2011 6:35 PM, aiswarya pawar wrote:
>
>> Hi users,
>>
>> Am running the mdru
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.
ns
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 Cerezo
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
Sender: gmx-users-boun...@gromacs.org
Date: Tue, 06 Dec 2011 13:30:55
To: Discussion
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 C
15
why is it saying that Timesteps at t=31 don't match (12, 26).
On Fri, Oct 21, 2011 at 12:25 PM, Mark Abraham wrote:
> 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
>> pa
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 lo
Hi,
All the parameters are ok, still i get the complex separated.
On Wed, Oct 19, 2011 at 7:02 PM, Justin A. Lemkul 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 the
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 Blac
i have N number of selection ie it should run as a batch. like its should
select group1: 0 and select group2: 32, this is 1st run then after this next
run should be select group1: 1 and select group2: 32 and so on.
On Wed, Sep 28, 2011 at 10:56 PM, Justin A. Lemkul wrote:
>
>
> aiswa
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 wrote:
>
>
> aiswarya pawar wrote:
>
>> Hi users,
>>
>> I have n number of program t
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 a
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 wrote:
> On 26/09/2011 5:10 PM, aiswarya pawar wrote:
>
>> HI Mark,
>>
>
, Sep 26, 2011 at 12:38 PM, Mark Abraham wrote:
> 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
>
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
http://li
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,
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 prot
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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Please search the archive at
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t 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
> wrote:
> > Hi users,
> >
> > The g_mindist gives the minimum dist
Hi users,
The g_mindist gives the minimum distance between the atoms other than the
actual distance.
Thanks
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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 g
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 wrote:
> On 13/09/2011 4:14 PM, aiswarya pawar wrote:
>
> Mark,
>
> the command
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 wrote:
> 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 d
, use -dist, but not together.
>
> -Justin
>
>
> Thanks
> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
>
> -Original Message-
> From: "Justin A. Lemkul"
> Sender: gmx-users-boun...@gromacs.org
> Date: Mon, 12
sers-boun...@gromacs.org
> Date: Mon, 12 Sep 2011 07:52:54
> To: Discussion list for GROMACS users
> Reply-To: jalem...@vt.edu,
> Discussion list for GROMACS users
> Subject: Re: [gmx-users] g_dist error
>
>
>
> aiswarya pawar wrote:
>> hi Justin,
>&
: [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 molecule th
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 wrote:
>
>
> aiswarya pawar wrote:
>
>> Hi gromacs Users,
>>
&g
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 wrote:
>
>
> aiswarya pawar wrote:
>
>> Hi Users,
>>
>&g
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 wrote:
>
>
> aiswarya pawar wrote:
>
>> Hi Users,
>>
>> Am using g_dist to f
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 .
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 arch
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 wrote:
> Hi users,
>
> To get the distanc
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
http://lists.
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 wrote:
> Hi users,
>
> To get the distance between water and protein i did -
>
> g_dist -f md.xtc -s md.tpr -o distance.x
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
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 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 able
lyse might be necessary for other criteria.
>
> Mark
>
>
> 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.co
this because
> this is usually related to chemical reactors in engineering and NOT in
> protein simulation )
> In your index-file you can index those molecules, which you need.
> Your equation does not make sense.
>
> >>> 24.08.11 16.01 Uhr >>>
> Mark,
>
nction (N(t) - N(t+r))dt
Where function(x-y) takes the value 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
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 the residence time of water.
Fir
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, s
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 Relianc
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:
> D
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 all,
Does Hydrogen bond existence in a time frame states the residence time of the
water molecule?
Thank you,
Aiswarya
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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
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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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.
Mark,
Sorry for the trouble.
Aiswarya
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-Original Message-
From: "Emanuel Peter"
Sender: gmx-users-boun...@gromacs.org
Date: Mon, 22 Aug 2011 12:36:02
To:
Reply-To: Discussion list for GROMACS users
Subject
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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