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 jalem...@vt.edu wrote: On 10/10/12 11:53 PM, Venkat Reddy wrote: Dear all, I am doing a protein-ligand simulation

[gmx-users] Regarding g_tune_pme optimization

as *'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 Laboratory

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

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 Department of Biotechnology IIT

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

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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department

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

where what you said is stated? it seems quite strange to me! 2012/11/12 Venkat Reddy venkat...@gmail.com Dear gromacs users, I have a very basic doubt regarding mdrun. Is there any difference between doing final MD for 100 ns at a stretch and doing the same with a 10 ns step size

[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

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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics

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

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 Computational

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 jalem...@vt.edu wrote: On 11/26/12 12:58 AM, Venkat Reddy wrote: Dear all, I am simulating a Protein-Drug complex. I am following Justin's

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 jalem...@vt.edu 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 linux. Regardless, the masses I pointed

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 jalem...@vt.edu wrote: On 11/26/12 9:12 AM, Venkat Reddy wrote

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

a fair amount of work to create a usable topology anyway. -Justin On Mon, Nov 26, 2012 at 7:46 PM, Justin Lemkul jalem...@vt.edu 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 linux

Re: [gmx-users] error during minimization

-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-600036 -- gmx-users mailing listgmx-users@gromacs.org http

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

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 Laboratory of Computational

[gmx-users] doubt regarding make_ndx

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 Wishes Venkat Reddy

[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 Department

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

/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 Reddy Chirasani PhD student Laboratory

[gmx-users] Radial density calculation

for 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

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 Madras Chennai INDIA-600036

[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

PM, Venkat Reddy venkat...@gmail.com 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: g_rdf -f file.trr -s file.pdb -n rdf.ndx -o rdf.xvg However, I get no data in the output rdf.xvg

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 mark.j.abra...@gmail.comwrote: On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy venkat...@gmail.com

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

. Kindly suggest how to go about solving this Thanks On Sat, Apr 6, 2013 at 2:26 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy venkat...@gmail.com wrote: There was no fatal error preceding the output. After selecting the groups

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

, or with all gromacs analysis utilities? On Mon, Apr 8, 2013 at 7:33 PM, Venkat Reddy venkat...@gmail.com wrote: Sir I loaded the trajectory. There doesn't seem to be anything wrong with it. Have no clue whats going wrong Thanks On Mon, Apr 8, 2013 at 5:28 PM, Dr. Vitaly Chaban vvcha

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

. Dr. Vitaly Chaban On Tue, Apr 9, 2013 at 7:44 AM, Venkat Reddy venkat...@gmail.com wrote: Sir I tried g_msd, after asking for group selection the program appears not to read the frames as it remains stuck at reading frame 0, time 0.00. What to do? Thanks

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

have been. As 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 venkat...@gmail.com wrote: Sir I truncated my file so it has only 10 molecules of water and 5 frames. gmxcheck

[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

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 student Laboratory

[gmx-users] Manual installation of new analysis tool

`grid_store':* *grid_mode.c:(.text+0x41a): undefined reference to `put_atom_in_box'* *collect2: ld returned 1 exit status* *make: *** [g_mydensity] Error 1* Please help me in this regard. Thanks for your valuable time and concern. -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory

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

24, 2013 at 8:14 AM, Venkat Reddy venkat...@gmail.com wrote: Dear all, I have got an analysis tool for analyzing membrane density from Dr.Luca monticelli. I have followed the installation instructions as given. 1) First thing is to load GROMACS $ *source /usr/local/gromacs/bin

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 venkat...@gmail.com wrote: Dear Mark Junghans, Thanks for your valuable suggestions. I have gone through the README file. It says

[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

it is not informative. Thank you so much for all the help On Tue, May 7, 2013 at 2:48 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: I think you can process the trajectories without generating TPR. Dr. Vitaly Chaban On Tue, May 7, 2013 at 12:12 PM, Venkat Reddy venkat...@gmail.com wrote: Dear

Re: [gmx-users] Usage of g_spatial

/Mailing_Lists -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 On Tue, May 7, 2013 at 6:23 PM, Christopher Neale chris.ne...@mail.utoronto.ca wrote: Try this: trjconv -s my.pdb -f

[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

Re: [gmx-users] residues interaction with ligand

-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-600036 -- gmx-users mailing listgmx-users@gromacs.org http

[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 post (un

[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 !

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.org/search before posting

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

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 Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD

[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 listgmx

[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 shar...@ccmb.res.in wrote: pdb2gmx -h sharada *-- Original Message --* From: Venkat Reddy venkat...@gmail.com

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

it... Sharada *-- Original Message --* From: Venkat Reddy venkat...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org 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 select the ss bonds. But after

[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-users mailing

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

Cheers from Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD -- check out the rest of the Windows LiveT. More than mail-Windows LiveT goes way beyond your inbox. More than messageshttp://www.microsoft.com/windows/windowslive

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

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 goes way beyond your inbox. More than messages

[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

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/mailman/listinfo

Re: [gmx-users] make_ndx option

)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 Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD

[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

[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

, there is no 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 jalem...@vt.edu wrote: On 8/1/13 12:07 PM, Venkat Reddy wrote: Dear Gmx-users, In the GROMACS site, it has been mentioned

[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

is 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

- 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 Sent: Monday, 19 August 2013 8:11 PM To: Discussion list for GROMACS

[gmx-users] Regarding g_densmap output

to 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

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 iitd...@gmail.comwrote: On Fri, Aug 30, 2013 at 11:18 AM, Venkat Reddy venkat...@gmail.com 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

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 Biotechnology IIT Madras

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 teemu.murt...@gmail.comwrote: Hello, On Sun, Sep 15, 2013 at 5:05 PM, Venkat Reddy venkat...@gmail.com wrote: I found g_sgangle is the suitable tool

Re: [gmx-users] Regarding g_sgangle index file

at 11:31 PM, Teemu Murtola teemu.murt...@gmail.comwrote: 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 venkat...@gmail.com wrote: On Tue, Sep

Re: [gmx-users] Regarding g_sgangle index file

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 teemu.murt...@gmail.comwrote: Hi, On Thu, Sep 19, 2013 at 7:19 PM, Venkat Reddy venkat

[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

vvcha...@gmail.comwrote: 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 venkat...@gmail.com wrote: Dear all, I have a basic doubt. Is there any difference between the two processes

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 tsje...@gmail.com wrote: Hi Venkat, It depends on what you mean with removing pbc. Cheers, Tsjerk On Sep 26, 2013 5:21 PM, Venkat Reddy venkat...@gmail.com wrote: Dear Sir

Re: [gmx-users] trjcat after trjconv

On Sep 26, 2013 6:46 PM, Venkat Reddy venkat...@gmail.com wrote: Dear Tsjerk sir, I used trjconv -pbc mol -ur compact options. On Thu, Sep 26, 2013 at 9:17 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Venkat, It... -- gmx-users mailing list gmx-users@gromacs.org http

Re: [gmx-users] trjcat after trjconv

Thank you sir. On Fri, Sep 27, 2013 at 11:47 AM, Tsjerk Wassenaar tsje...@gmail.comwrote: Yes. Cheers, Tsjerk On Fri, Sep 27, 2013 at 7:51 AM, Venkat Reddy venkat...@gmail.com wrote: Thanks for the quick reply sir. So, does it mean I can apply trjcat on the processed xtc files

[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 Department

Re: [gmx-users] parallel simulation

...@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-600036 -- gmx-users mailing listgmx-users@gromacs.org http

[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

by default. Dr. Vitaly V. Chaban On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy venkat...@gmail.com 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 using g_msd (or any other

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 jalem...@vt.edu 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.xvg -tu ns

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

do the same thing? Moreover, mine is a coarse-grained system. On Tue, Nov 12, 2013 at 9:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/12/13 11:25 AM, Venkat Reddy wrote: Then, how to mention the direction for spherical particles Sir? Read g_msd -h again, paying specific attention

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 jalem...@vt.edu wrote: On 11/12/13 12:30 PM, Venkat Reddy wrote: Dear Sir, Thanks for the quick reply. So, I have

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

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: Thanks Justin. So, I have to calculate diffusion coefficient three times (x,y,z) and finally

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 jalem...@vt.edu wrote: On 11/13/13 12:20 AM, Venkat Reddy wrote: Dear Justin and Piggot, Thanks