ch the archive at http://www.gromacs.org/search before posting!
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> www interface or send it to gmx-users-requ...@gromacs.org.
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With Best Wishes
V
441 457
459 463
then I renamed the index file using
> name 26 tunnel
>q
When I checked back my index file, I found some water molecule atoms also
inserted in the tunnel group. What could be the problem?
Am I doing in the proper way?
Thanks a lot for your valuable time.
--
With Best Wish
Dear all,
Are the topologies generated for lipids by ATB accurate enough?
(I have mentioned the molecule type as "*Lipid*" prior to submission to ATB)
Thanks for your valuable time
With best wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Dep
t: Re: [gmx-users] Gromos43A1-S3 lipid parameters
> >
> >
> >
> > On 2/28/13 2:16 AM, Venkat Reddy wrote:
> > > Dear all,
> > > Can I use Gromos43A1-S3 lipid parameters provided in the GROMACS site
> > > along with the GROMOS53a6 forcefield in t
your valuable time
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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re posting!
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Venkat Reddy Chirasani
PhD student
Laboratory of
parameters, I do not know how to go about generating
a tpr file (in case that is the problem). The rdf.ndx file is correct for
my atom selection. Please suggest how to go about solving this.
Thank you
--
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department
2:41 AM, Justin Lemkul wrote:
> On Fri, Apr 5, 2013 at 2:30 PM, Venkat Reddy wrote:
>
> > Dear users
> >
> > I have used AMBER MD package to run simulation for a solvent box. I am
> now
> > using the gromacs utility to calculate rdf as follows:
> >
>
Sir
I was using an old version. Now I used 4.5.5, it still gives me the same
blank output file.
Kindly suggest how to go about solving this
Thanks
On Sat, Apr 6, 2013 at 2:26 PM, Mark Abraham wrote:
> On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy wrote:
>
> > There was no
5.5, it still gives me the same
> > blank output file.
> >
> > Kindly suggest how to go about solving this
> >
> > Thanks
> >
> >
> > On Sat, Apr 6, 2013 at 2:26 PM, Mark Abraham > >wrote:
> >
> > > On Sat, Apr 6, 2013 at 7:1
all gromacs
> analysis utilities?
>
>
> On Mon, Apr 8, 2013 at 7:33 PM, Venkat Reddy wrote:
>
>> Sir
>>
>> I loaded the trajectory. There doesn't seem to be anything wrong with it.
>> Have no clue whats going wrong
>>
>> Thanks
>>
>&g
> the
> > right place -- just a guess.
> >
> > Dr. Vitaly Chaban
> >
> >
> >
> >
> > On Tue, Apr 9, 2013 at 7:44 AM, Venkat Reddy
> wrote:
> >
> >> Sir
> >>
> >> I tried g_msd, after asking for group selec
s you can see with g_rdf -h, it defaults to using periodic boundary
> conditions. You need to do something different.
>
> Mark
>
>
> On Wed, Apr 10, 2013 at 2:38 PM, Venkat Reddy wrote:
>
>> Sir
>>
>> I truncated my file so it has only 10 molecules of wat
I
am using it now, spatial distribution of all the anions in simulation box
is shown, which is very inconclusive. I cannot specify a particular set of
cations and anions, as they separate over time.
Please help
--
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational
D in
cg2aa
conversion. Can we use it for pure lipid systems (say
POPC+CHOL+triglyceride+CE)?
When I tried to execute it, I am getting the following error
"Cannot open angles for reading: No such file or directory"
Thanks for your concern
--
With Best Wishes
Venkat Reddy Chirasani
PhD s
t+0x8f1): undefined reference to `save_free'*
*dist_mode.c:(.text+0x917): undefined reference to `save_free'*
*dist_mode.c:(.text+0x948): undefined reference to `save_free'*
*grid_mode.o: In function `build_grids':*
*grid_mode.c:(.text+0x81): undefined reference to `save_calloc
> Subject: Re: [gmx-users] Manual installation of new analysis tool
> > To: Discussion list for GROMACS users
> > Message-ID:
> > 4wko947kc_y7s_gsyrxg8nms...@mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > On Wed, Apr
Dear Mark & Junghans,
I have got it. There is some problem in the Makefile. Thanks for your
suggestions and help
On Fri, Apr 26, 2013 at 11:12 AM, Venkat Reddy wrote:
> Dear Mark & Junghans,
> Thanks for your valuable suggestions.
> I have gone through the README file. It s
command needs
pre-processing of the coordinates (Steps 1 and 2 in g_spatial help) but I
need tpr file for that. So there is no way of doing g_spatial without a
tpr file is it? Then how do I generate tpr file for my system?
Thanks for all the help
--
With Best Wishes
Venkat Reddy Chirasani
PhD
not informative.
Thank you so much for all the help
On Tue, May 7, 2013 at 2:48 PM, Dr. Vitaly Chaban wrote:
> I think you can process the trajectories without generating TPR.
>
> Dr. Vitaly Chaban
>
>
> On Tue, May 7, 2013 at 12:12 PM, Venkat Reddy wrote:
>
> > Dear
s to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madra
Dear all,
How can I generate a particular lipid itp file compatible with CHARMM27
(say Cholesteryl oleate). The link for CHARMM compatible cholesterol
parameters in *lipidbook *website is
also dead.
Thanks a lot
--
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational
Dear all,
How can I generate a particular lipid itp file compatible with CHARMM27
(say Cholesteryl oleate). The link for CHARMM compatible cholesterol
parameters in the lipidbook website is
also dead.
Thanks a lot
--
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of
ost (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Depa
am using
Gromacs-4.5.5.
Thank you
--
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Thanks Justin for the information. By the way, Could you please give me a
hint on the release of new GPU-version (4.6)?
On Thu, Oct 11, 2012 at 4:20 PM, Justin Lemkul wrote:
>
>
> On 10/10/12 11:53 PM, Venkat Reddy wrote:
>
>> Dear all,
>> I am doing a protein-ligand
*'0'*. My doubt is, how could
it be possible to get best performance without dedicated PME nodes?
2) What could be the optimum value for *-rcom *to get the best performance
on a super cluster (*i.e., 256 nodes*)?
Thanks in advance
With Best Wishes
Venkat Reddy Chirasani
PhD student
here that continuous MD of longer simulations
will cause spurious drifts in velocity and energy, errors in velocity
correlationetc. Please advise me in this regard.
Thank you and Happy DIWALI
--
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Departm
>
>>>
> --
> Ananya Chatterjee,
> Senior Research Fellow (SRF),
> Department of biological Science,
> IISER-Kolkata.
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/l
what you said is stated?
> it seems quite strange to me!
>
>
>
> 2012/11/12 Venkat Reddy
>
> > Dear gromacs users,
> >
> > I have a very basic doubt regarding mdrun. Is there any difference
> between
> > "doing final MD for 100 ns at a stretc
Dear Gromacs users,
How to launch mdrun_mpi using g_tune_pme on a cluster, because
*
*
*g_tune_pme -launch *launches mdrun but not mdrun_mpi.
Thanks for your valuable time
--
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
ch>before
> posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read
> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
&g
9 15.9994
45OA 1 ORP O2 8 -0.466 15.9994
46 CH2 1 ORP C13 80.292 14.0270
*47 CH3 1 ORP C14 9 -0.064 15.0350*
Thanks for your valuable time
--
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Com
Dear Justin,
I haven't touched the *Mass column.* I have edited the charges only using
"gedit" in linux.
On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul wrote:
>
>
> On 11/26/12 12:58 AM, Venkat Reddy wrote:
>
>> Dear all,
>> I am simulating a Protei
Thanks Justin...I will certainly do.
On Mon, Nov 26, 2012 at 7:46 PM, Justin Lemkul wrote:
>
>
> On 11/26/12 9:12 AM, Venkat Reddy wrote:
>
>> Dear Justin,
>> I haven't touched the *Mass column.* I have edited the charges only using
>> "gedit" in li
Dear Justin,
One more doubt. I am using Gromos 53A6 ff. Can I use Prodrg to generate
topology for my ligand? Because, I guess, prodrg uses Gromos 43A1. Can I
mix 53A6 and 43A1?
On Mon, Nov 26, 2012 at 7:46 PM, Justin Lemkul wrote:
>
>
> On 11/26/12 9:12 AM, Venkat Reddy wrote:
>
&g
Thank yo Justin for your help...I have generated the same topology using *ATB.
*Now, I got the masses correctly (as pointed out by you). So, I'm afraid
that is there any bug in PRODRG server?
On Mon, Nov 26, 2012 at 8:09 PM, Justin Lemkul wrote:
>
>
> On 11/26/12 9:35 AM, Venk
he
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-60
s.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
With Best Wishes
Venkat Red
Hai Sir !
This is Venkat Reddy, from the University Of Hyderabd,pursuing M.Tech
Bioinformatics. Iam Currently using GROMACS in my project work. I got an
error. It states that
Range Checking error :
Explanation: During Neibor searching, we assign each particle to a grid
based on its
hanking you sir
Urs sincerely
Venkat Reddy Chirasani
M.Tech Bioinformatics
UNIVERSITY OF HYDERABAD
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Please search the archive at http://www.gromacs.org/search before posting!
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how to save the coordinates of atoms at regular intervals that were
generated during "mdrun" ?? Is it automatic or we need to modify .mdp file
????
Venkat Reddy Chirasani
M.Tech Bioinformatics
UNIVERSITY OF HYDERABAD
___
gmx-users mailing l
Hai Every one ! Is it possible to break a disulfide bridge using gromacs
?If so,Can anybody suggest me, how to do it???
Thanks for ur valuable time
With best wishes
Venkat Reddy Chirasani
M.Tech Bioinformatics
UNIVERSITY OF HYDERABAD
Hai !
with "pdb2gmx -ss", i can select the ss bonds. But after that, how to break
a particular ss bond (not all).
Thank you
On Fri, Mar 6, 2009 at 11:01 AM, sharada wrote:
>
> pdb2gmx -h
>
> sharada
>
>
> *-- Original Message --*
> From: Venkat Reddy
it...
>
> Sharada
>
> *-- Original Message --*
> From: Venkat Reddy
> To: Discussion list for GROMACS users
> Date: Fri, 6 Mar 2009 11:31:57 +0530
> Subject: Re: [gmx-users] How to break a disulfide bond ???
>
> Hai !
>
> with "pdb2gmx -ss", i can sele
Hi Everyone !
How can i see the variations in the "Cβ-S-S-Cβ" (Disulfide bridge) dihedral
angle during a simulation ?
Thanks in advance
Cheers from
Venkat Reddy Chirasani
M.Tech Bioinformatics
UNIVERSITY OF HYDERABAD
___
gmx-use
angle during a simulation ?
> Thanks in advance
>
>
>
>
> Cheers from
> Venkat Reddy Chirasani
> M.Tech Bioinformatics
> UNIVERSITY OF HYDERABAD
>
> --
> check out the rest of the Windows LiveT. More than mail-Windows LiveT goe
: [gmx-users] How to calculate the dihedral angle variations ???
> >>
> >> Hi Everyone !
> >> How can i see the variations in the "Cβ-S-S-Cβ" (Disulfide bridge)
> >> dihedral angle during a simulation ?
> >> Thanks in advance
>
Hai Everyone ! I hav a small doubt regarding RMSF . How can we calculate
rmsf for helices and sheets only in a protein (excluding loops )???
Thanks for ur valuable time.
--
With Best Wishes
Venkat Reddy Chirasani
M.Tech Bioinformatics
UNIVERSITY OF HYDERABAD
given some different error like *atom type NR is not
found *(I suppose this is due to the ligand topology generated by PRODRG).
Please help me in this regard.
Thanking you
With Best Wishes
Venkat Reddy Chirasani
IITM
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.
Thanking you
With Best Wishes
Venkat Reddy Chirasani
IIT Madras
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Please don't pos
renumber from
2-17?
Thank you
--
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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* Please
bilayer, infact, only few bound lipids are there. In which
direction I should choose the normal (*-d option*)?
On Thu, Aug 1, 2013 at 10:54 PM, Justin Lemkul wrote:
>
>
> On 8/1/13 12:07 PM, Venkat Reddy wrote:
>
>> Dear Gmx-users,
>> In the GROMACS site, it has been m
Dear All,
I would like to convert my NAMD psf file to GROMACS tpr file? First of all,
is it possible? If so, is there any script available?
Please help me in this regard.
Thanks for your valuable time.
--
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
larger, the integration of it should give
a higher value right?
Please help.
--
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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http
.war...@monash.edu
> +61 3 9903 9304
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
> > -Original Message-
> > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> > boun...@gromacs.org] On Behalf Of Venkat Reddy
analyze
this text file? Also Please suggest me any tool which can convert this text
file to some visually appealing grid map or a 2D (or) 3D graph?
Thanks for your valuable time
--
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of
But its not a xpm file. Its a dat file
On Fri, Aug 30, 2013 at 12:05 PM, Chandan Choudhury wrote:
> On Fri, Aug 30, 2013 at 11:18 AM, Venkat Reddy
> wrote:
>
> > Dear Gromacs users,
> > I am analyzing the density of my spherical lipid vesicle using g_densmap
> > tool
ute g_sgangle, it is saying something wrong with the index
file. How to solve this error?
How to organize the index file in a multiple of 2?
Thank you for your valuable time and concern
--
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biot
Thank you sir for the nice tip. I will try it out and let you know if I
have any problem.
On Tue, Sep 17, 2013 at 12:38 AM, Teemu Murtola wrote:
> Hello,
>
> On Sun, Sep 15, 2013 at 5:05 PM, Venkat Reddy wrote:
>
> > I found g_sgangle is the suitable tool
> > to calcula
p 17, 2013 at 11:31 PM, Teemu Murtola wrote:
> Hello,
>
> Please keep correspondence on the list so that others may benefit from it,
> and you don't need to wait for some particular person to respond.
>
> On Tue, Sep 17, 2013 at 1:24 PM, Venkat Reddy wrote:
> >
>
utput. My command is:
gmx gangle -f traj_noPBC.xtc -s topol.tpr -n -g1 vector -g2 vector -group1
'resname CHOL and name R5 R0' -group2 'resname CHOL and name R5 R0' -oav
-oall -oh
On Mon, Sep 23, 2013 at 11:19 PM, Teemu Murtola wrote:
> Hi,
>
> On Thu, Sep 19, 2013
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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wrote:
> I do not think that I ever tried myself, but is seems all the same.
> Why do you ask?
>
>
> Dr. Vitaly V. Chaban
>
>
> On Thu, Sep 26, 2013 at 3:40 PM, Venkat Reddy wrote:
> > Dear all,
> > I have a basic doubt. Is there any difference between the two proc
Dear Tsjerk sir,
I used trjconv -pbc mol -ur compact options.
On Thu, Sep 26, 2013 at 9:17 PM, Tsjerk Wassenaar wrote:
> Hi Venkat,
>
> It depends on what you mean with "removing pbc".
>
> Cheers,
>
> Tsjerk
>
> On Sep 26, 2013 5:21 PM, "Venkat Red
jump.
>
> Cheers,
>
> Tsjerk
>
> On Sep 26, 2013 6:46 PM, "Venkat Reddy" wrote:
>
> Dear Tsjerk sir,
> I used trjconv -pbc mol -ur compact options.
>
> On Thu, Sep 26, 2013 at 9:17 PM, Tsjerk Wassenaar
> wrote: > Hi Venkat, > > It...
>
&
Thank you sir.
On Fri, Sep 27, 2013 at 11:47 AM, Tsjerk Wassenaar wrote:
> Yes.
>
> Cheers,
>
> Tsjerk
>
>
> On Fri, Sep 27, 2013 at 7:51 AM, Venkat Reddy wrote:
>
> > Thanks for the quick reply sir.
> > So, does it mean I can apply "trjcat"
Dear all,
I have a basic doubt regrading g_membed.
Is it compulsory to solvate the membrane system before the protein's
insertion or can we solvate after the protein's insertion?
--
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Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Dep
h before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
With Best Wishes
Venkat Reddy Chirasani
PhD student
Dear all,
I am simulating a spherical lipid vesicle. I want to calculate the
diffusion coefficient for each lipid component in 3D. How to calculate it
using g_msd (or any other tool like g_velacc)?
Thank you for your concern
--
With Best Wishes
Venkat Reddy Chirasani
--
gmx-users mailing list
ult.
>
>
> Dr. Vitaly V. Chaban
>
>
> On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy wrote:
> > Dear all,
> > I am simulating a spherical lipid vesicle. I want to calculate the
> > diffusion coefficient for each lipid component in 3D. How to calculate it
> >
Then, how to mention the direction for spherical particles Sir?
On Tue, Nov 12, 2013 at 7:28 PM, Justin Lemkul wrote:
>
>
> On 11/12/13 8:55 AM, Venkat Reddy wrote:
>
>> Thank you sir for the prompt reply.
>> *g_msd -f traj.xtc -s topol.tpr -n msd.ndx -lateral z -o msd.
so shall I do the
same thing? Moreover, mine is a coarse-grained system.
On Tue, Nov 12, 2013 at 9:57 PM, Justin Lemkul wrote:
>
>
> On 11/12/13 11:25 AM, Venkat Reddy wrote:
>
>> Then, how to mention the direction for spherical particles Sir?
>>
>>
> Read g_msd
Thanks Justin. So, I have to calculate diffusion coefficient three times
(x,y,z) and finally add-up together to get in 3D???
On Tue, Nov 12, 2013 at 11:25 PM, Justin Lemkul wrote:
>
>
> On 11/12/13 12:30 PM, Venkat Reddy wrote:
>
>> Dear Sir, Thanks for the quick reply
, so I suggest you search the literature for
> papers simulating vesicles to see how the lipid diffusion was calculated.
>
> Cheers
>
> Tom
>
>
> On 11/12/2013 06:35 PM, Justin Lemkul wrote:
>
>>
>>
>> On 11/12/13 1:33 PM, Venkat Reddy wrote:
>>
>>
diffusion coefficient to the surface lipids (diffusion
along the lipid-water interface
) and 3D diffusion coefficient to the core lipids.
On Wed, Nov 13, 2013 at 7:19 PM, Justin Lemkul wrote:
>
>
> On 11/13/13 12:20 AM, Venkat Reddy wrote:
>
>> Dear Justin and Piggot,
>> Th
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