Re: [gmx-users] make_ndx option

ch the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- With Best Wishes V

[gmx-users] doubt regarding make_ndx

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

[gmx-users] Lipid topologies generated by ATB

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

Re: [gmx-users] Gromos43A1-S3 lipid parameters

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

[gmx-users] Radial density calculation

your valuable time With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive

Re: [gmx-users] Radial density calculation

re 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 Laboratory of

[gmx-users] RDF output has no data

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

Re: [gmx-users] RDF output has no data

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: > > >

Re: [gmx-users] RDF output has no data

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

Re: [gmx-users] Re: RDF output has no data

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

Re: [gmx-users] Re: RDF output has no data

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

Re: [gmx-users] Re: RDF output has no data

> 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

Re: [gmx-users] Re: RDF output has no data

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

[gmx-users] Plotting data from g_spatial

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

[gmx-users] Regarding top2psf script

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

[gmx-users] Manual installation of new analysis tool

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

Re: [gmx-users] Re: Manual installation of new analysis tool

> 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

Re: [gmx-users] Re: Manual installation of new analysis tool

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

[gmx-users] Usage of g_spatial

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

Re: [gmx-users] Usage of g_spatial

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

Re: [gmx-users] Usage of g_spatial

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

[gmx-users] Cholesteryl oleate parameters for CHARMM27 ff in Gromacs

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

[gmx-users] CHARMM lipid parameters

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

Re: [gmx-users] residues interaction with ligand

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

[gmx-users] Regarding mdrun

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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] Confusion in passing check point file

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

[gmx-users] Regarding g_tune_pme optimization

*'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

[gmx-users] Continuous mdrun vs step-by-step mdrun

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

Re: [gmx-users] how to restart a stopped simulation

> >>> > -- > 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

Re: [gmx-users] Continuous mdrun vs step-by-step mdrun

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

[gmx-users] How to launch mdrun_mpi using g_tune_pme on a cluster

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

Re: [gmx-users] problem in running md simulation

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

[gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0

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

Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0

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

Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0

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

Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0

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

Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0

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

Re: [gmx-users] error during minimization

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

Re: [gmx-users] gen-vel=no

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

[gmx-users] Regarding an Error !

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

[gmx-users] Hai Sir !

hanking you sir Urs sincerely Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.or

Re: [gmx-users] Gromacs 4 with mpi interface

Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Venkat

[gmx-users] Dear Sir !

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

[gmx-users] How to break a disulfide bond ???

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

Re: [gmx-users] How to break a disulfide bond ???

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

Re: Re: Re: [gmx-users] How to break a disulfide bond ???

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

[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 Cheers from Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD ___ gmx-use

Re: [gmx-users] How to calculate the dihedral angle variations ???

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

Re: [gmx-users] How to calculate the dihedral angle variations ???

: [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 >

[gmx-users] Regarding RMSF !

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

[gmx-users] Problem in the inclusion of Potassium ion topology

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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailma

[gmx-users] CG representation for Organic molecules

. Thanking you With Best Wishes Venkat Reddy Chirasani IIT Madras -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't pos

[gmx-users] Regarding g_order

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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please

Re: [gmx-users] Regarding g_order

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

[gmx-users] psf to tpr

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

[gmx-users] Coordination number

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 -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Coordination number

.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

[gmx-users] Regarding g_densmap output

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

Re: [gmx-users] Regarding g_densmap output

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

[gmx-users] Regarding g_sgangle index file

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

Re: [gmx-users] Regarding g_sgangle index file

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

Re: [gmx-users] Regarding g_sgangle index file

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: > > >

Re: [gmx-users] Regarding g_sgangle index file

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

[gmx-users] trjcat after trjconv

Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org

Re: [gmx-users] trjcat after trjconv

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

Re: [gmx-users] trjcat after trjconv

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

Re: [gmx-users] trjcat after trjconv

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... > &

Re: [gmx-users] trjcat after trjconv

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"

[gmx-users] Regarding g_membed

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? -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Dep

Re: [gmx-users] parallel simulation

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

[gmx-users] Calculating diffusion coefficient in three dimension

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

Re: [gmx-users] Calculating diffusion coefficient in three dimension

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 > >

Re: [gmx-users] Calculating diffusion coefficient in three dimension

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.

Re: [gmx-users] Calculating diffusion coefficient in three dimension

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

Re: [gmx-users] Calculating diffusion coefficient in three dimension

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

Re: [gmx-users] Calculating diffusion coefficient in three dimension

, 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: >> >>

Re: [gmx-users] Calculating diffusion coefficient in three dimension

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