[gmx-users] Persistence length of whole DNA molecule

Hi all, I want to calculate the persistence length of whole DNA molecule. I know that we can calculate it by using option g_polystat -f .trr -p p.xvg , but I am not able to figure out what set of of atoms I have to select while making the index, so that I could get persistence length o

Re: [gmx-users] Re: Simulating a semi-membrane protein

On 7/22/13 10:21 PM, pavithrakb wrote: Dear Sir, Thank you. I understand it now. But, when apply the force field, should I select the membrane ff like gromos56 (like in your KALP tutorial) or will it be a complex process to select a ff? Choosing a force field is always complicated. There ar

[gmx-users] how to remove some molecules

Dear gmx-users I would like to calculate the PMF in a system composed of nanotube+surfactants. for doing this I use the final configuration of previous surfactant adsorption simulation onto carbon nanotube. the problem is I want to remove some of non-adsorbed surfactant molecules. Would you please

Re: [gmx-users] how to remove some molecules

On 7/23/13 5:40 AM, niaz poorgholami wrote: Dear gmx-users I would like to calculate the PMF in a system composed of nanotube+surfactants. for doing this I use the final configuration of previous surfactant adsorption simulation onto carbon nanotube. the problem is I want to remove some of non

[gmx-users] how to remove some molecules

Thank you Sir for your reply. but I do not know how to recognize the non-adsorbed molecules in a gro file? Is there any way to recognize them in a gro file( I have seen the in VMD)? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please sear

Re: [gmx-users] gpu cluster explanation

Hi Richard, Thank you for the help and sorry for the delay in my reply. I tried some test run changing some parameters (e.g. removing PME) and I was able to reach 20ns/day, so I think that 9-11 ns/day it's the max that I can obtain for my setting. thank your again for your help. cheers, Fra On

[gmx-users] storage problem during a simulation

Hi all, This morning the gpu cluster that I'm using had some troubles with the network connection between nodes that deny access to the storage. Now, the simulations are still running and it seems that during the "shut down" mdrun wrote a lot of checkpoints and restarted the simulation once the com

[gmx-users] Rotation Constraints - PMF

Dear user and expert, I'd like ask you a suggestion about a problem that I will try present you schematically. I have got a structure "s" and I have generated the topolgy file itp for it.A number of separate "s" in turn generate a complex structure A, that is characterized by a cylindrical shape

Re: [gmx-users] Persistence length of whole DNA molecule

Hi, I have not used g_polystat, and I cannot say about usage of this tool. I observed that you missed two oxygen atoms (O3' and O5') in the backbone atom index. There are several methods for the calculation of persistence length of a polymer, and you may look into literature for theories. For exa

Re: [gmx-users] Persistence length of whole DNA molecule

Thank you sir for a reply , I missed those atoms , I will try to replace it and then do it. The out put file contains not length but bonds, It says average persistence length is 4.3 bonds. I do not know how to calculate helical axis, I will try today using 3DNA and let you know. Thank you very

Re: [gmx-users] how to remove some molecules

On 7/23/13 5:56 AM, niaz poorgholami wrote: Thank you Sir for your reply. but I do not know how to recognize the non-adsorbed molecules in a gro file? Is there any way to recognize them in a gro file( I have seen the in VMD)? Label them by name in VMD. -Justin -- ==

Re: [gmx-users] Rotation Constraints - PMF

Hi Anna, please have a look at the Enforced Rotation Section in the Gromacs 4.6 manual. You can restrain the angle of rotation about an axis by setting the rotation rate to zero. There is also a 4.5 add-on available with rotational restraints in the Gromacs git repository (branch "rotation"). For

[gmx-users] Re: Simulating a semi-membrane protein

Sir, I'm new to simulation. is there any papers or materials (book or website) to learn about the forcefields and their limitations. All the advice I get from people is to select a ff and membrane based on the previous works on that protein or protein family. I know its too much to ask but, can you

Re: [gmx-users] Re: Simulating a semi-membrane protein

On 7/23/13 7:46 AM, pavithrakb wrote: Sir, I'm new to simulation. is there any papers or materials (book or website) to learn about the forcefields and their limitations. All the advice I get from people is to select a ff and membrane based on the previous works on that protein or protein famil

Re: [gmx-users] Re: Simulating a semi-membrane protein

Dear Pavithrakb, First of all, your choice will depend on the available parameters for the lipid molecules that you want to simulate (check the Lipidbook repository ). Concerning the GROMOS force fields the most recent lipid parameters are the ones included in th

RE: [gmx-users] Calculate interaction energy dynamically

Thanks so much for the suggestion. By using the command: trjorder -f system.trr -s system.tpr -n system.ndx -da 3 -na 12 -r 2.0 -o system_ordered.trr the resulting system_ordered.trr indeed contained lipids 2,3,4... in the closest proximity to lipid 1 (within the specified cuttoff of 2.0 nm).

[gmx-users] Getting a .tpr file for C-alpha atoms from an all atom .tpr file

Hello All, I there any way to get a .tpr for C-alpha atoms from an all atom .tpr file. -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.g

Re: [gmx-users] Getting a .tpr file for C-alpha atoms from an all atom .tpr file

On 7/23/13 11:58 AM, bipin singh wrote: Hello All, I there any way to get a .tpr for C-alpha atoms from an all atom .tpr file. tpbconv -h, particularly point 3. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharma

Re: [gmx-users] Calculate interaction energy dynamically

On 7/23/13 11:05 AM, Davit Hakobyan wrote: Thanks so much for the suggestion. By using the command: trjorder -f system.trr -s system.tpr -n system.ndx -da 3 -na 12 -r 2.0 -o system_ordered.trr the resulting system_ordered.trr indeed contained lipids 2,3,4... in the closest proximity to lip

RE: [gmx-users] Calculate interaction energy dynamically

Thank you very much for your continuous support. > Date: Tue, 23 Jul 2013 12:06:57 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Calculate interaction energy dynamically > > > > On 7/23/13 11:05 AM, Davit Hakobyan wrote: > > Thanks so much for the suggesti

[gmx-users] Re: gmx-users Digest, Vol 111, Issue 101

Dear Justin, Thank you for your suggestion... Best regards Collins On Mon, Jul 22, 2013 at 10:00 AM, wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mail

[gmx-users] GROMACS benchmarks (d.dppc, d.lzm, etc.) with V4.6.1

Hi Folks, I can't seem to get the GROMACS benchmarks to work with 4.6.1. They work fine with 4.5.5. Can anyone offer any suggestion? It dies in grompp first with the following: --- Program grompp_mpi, VERSION 4.6.1 Source code file: /lustre/tucc

Re: [gmx-users] storage problem during a simulation

What does gmxcheck have to say about your output files? On Jul 23, 2013 12:17 PM, "Francesco" wrote: > Hi all, > This morning the gpu cluster that I'm using had some troubles with the > network connection between nodes that deny access to the storage. > Now, the simulations are still running and

Re: [gmx-users] storage problem during a simulation

the simulations are still running, they should end tomorrow afternoon. Fra On Tue, 23 Jul 2013, at 06:26 PM, Mark Abraham wrote: > What does gmxcheck have to say about your output files? > On Jul 23, 2013 12:17 PM, "Francesco" wrote: > > > Hi all, > > This morning the gpu cluster that I'm using

Re: [gmx-users] storage problem during a simulation

gmxcheck can still read your output files safely. :-) On Tue, Jul 23, 2013 at 10:26 PM, Francesco wrote: > the simulations are still running, they should end tomorrow afternoon. > > Fra > > On Tue, 23 Jul 2013, at 06:26 PM, Mark Abraham wrote: >> What does gmxcheck have to say about your output f

Re: [gmx-users] Calculate interaction energy dynamically

On 7/23/13 1:54 PM, Davit Hakobyan wrote: Thank you very much for your continuous support. Date: Tue, 23 Jul 2013 12:06:57 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Calculate interaction energy dynamically On 7/23/13 11:05 AM, Davit Hakobyan wrote: Tha

[gmx-users] Re: Simulating a semi-membrane protein

Thank you both of you for taking time to help me.. This would be definitely useful. thank you so much. -- View this message in context: http://gromacs.5086.x6.nabble.com/Simulating-a-semi-membrane-protein-tp5010032p5010063.html Sent from the GROMACS Users Forum mailing list archive at Nabble.

[gmx-users] OpenSuse 12.1 + CUDA Installation Error

*Hi,* *I keep getting errors when I try to install gromacs in OpenSuse 12.1.* *I have installed cuda 5.0 and the nvidia cards. **I have tried with different parameters for cmake:* >cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda *When I make, this error appear

[gmx-users] freez gropus

I am doing simulation of metal clusters with membranes by position restrain (with f=1000) the membrane. In this simulation the structure of metal cluster is collapsed after entering into membrane. I want to preserves its structure with out doing position restrain the metal cluster because it has to

[gmx-users] Re: editconf: Invalid command line argument: –f

Yep, the pdf was not written or copy and pasted the "-" incorrectly. Thanks :) -Jonathan On Fri, Jul 12, 2013 at 3:03 PM, Jonathan Saboury wrote: > I am following "Tutorial 1" from > https://extras.csc.fi/chem/courses/gmx2007/tutorial1/index.html > > I try the command "editconf –f conf.gro –b

[gmx-users] Limitations of simulations?

I just finished this tutorial and found it very informative: http://cinjweb.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf However, This was based on a complex from a pdb. I was wondering if it was possible to just simulate the protein without complex and put the ligand as a solute and actually

RE: [gmx-users] Limitations of simulations?

I would like to stop to receive this e-mail, how can i procide?Thanks Fábio Filippi MatioliGraduando em Física MédicaUNESP-BotucatuTel (19) 9291.6738 > Date: Tue, 23 Jul 2013 22:57:29 -0700 > From: jsab...@gmail.com > To: gmx-users@gromacs.org > Subject: [gmx-users] Limitations of simulations? >

[gmx-users] membrane simulations

I am doing simulation of metal clusters with membranes by position restrain (with f=1000) the membrane. In this simulation the structure of metal cluster is collapsed after entering into membrane. I want to preserves its structure with out doing position restrain the metal cluster because it has to