[gmx-users] nstxout, nstvout, . . .

: You need to re submit the jobs, with decreased time. And next time check with the manual and consider your needs before making arbitrary choices :-) Mark   -- Chandan kumar Choudhury NCL, Pune INDIA On Sat, Apr 6, 2013 at 11:20 AM, dina dusti dinadu...@yahoo.com wrote: Dear Specialists

[gmx-users] nstxout, nstvout, . . .

Thanks from your help. Best Regards Dina From: Mark Abraham mark.j.abra...@gmail.com To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, April 6, 2013 1:27 PM Subject: Re: [gmx-users] nstxout, nstvout

[gmx-users] nstxout, nstvout, . . .

Dear Specialists I am a beginner at Gromacs. I work with MARTINI CG force field. I selected 5 for nstxout        = 5    nstvout        = 5        nstenergy    = 5 nstlog        = 5    nstxtcout    = 5 and my jobs have been finished. I found that this

[gmx-users] concatenate of .edr files

Dear GROMACS Users, I have simulations with 120 ps and the file names are md.*, then I expended the time of simulation to 240 ps, with file names next as are follow: tpbconv -s md.tpr -extend 120 -o next.tpr mdrun -v -deffnm next -s next.tpr -cpi md.cpt I use from trjcat to

[gmx-users] concatenate of .edr files

Dear Justin, Thank you very much from your help. Best Regards Dina - Original Message - From: Justin Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, January 19, 2013 3:16 PM Subject: Re: [gmx

[gmx-users] dipole moment

Dear GROMACS Specialists, I have one system consists of water and two other molecules. I work by MARTINI CG force field. I want to calculate dipole moment of molecules in water. May I ask you to help me, Please? Best Regards Dina -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] dipole moment

Dear Justin, Thank you very much from your response. Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, May 13, 2012 5:23 PM Subject: Re: [gmx

[gmx-users] radius of gyration

Dear GROMACS Specialists, I have one question about radius of gyration for micelle, Please help me. My micelle is created at 10 ps by Martini CG force field. When I calculate the radius of gyration from this time as g_gyrate -f 1.xtc -s 1.tpr -n 1.ndx -o gyrate.xvg -b 10 and g_analyze -f

[gmx-users] radius of gyration

Dear Justin, Thank you very much from your help. Yes, the micelle was created after 100 ns from start of simulation. If the first procedure is true, so why the error estimate is so small and why the error estimate of Rg is so different with Rg(x,y,z)? Please help me. Best Regards Dina --

[gmx-users] radius of gyration

...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, May 9, 2012 12:44 AM Subject: Re: [gmx-users] radius of gyration On 5/8/12 4:08 PM, dina dusti wrote: Dear Justin, Thank you very much from your help. Yes, the micelle

[gmx-users] radius of gyration

Dear Justin, Thank you very much from your response. Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, May 9, 2012 4:52 AM Subject: Re: [gmx

[gmx-users] the radius of dry core

Dear Dr. Warren, Thank you very much from your help. Best Regards Dina -- 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

[gmx-users] error estimate

Dear GROMACS Specialists, I have doubt about these error estimates for Rg and Rg(x,y,z). May I ask you to say me why is the difference between them. for example for Rg is 0.0002 and for others is 0.00x?! And are my error estimates true? Please help me.  

[gmx-users] the radius of dry core

Dear Dr. Warren, Thank you very much from your help, but I want to calculate the fraction of methylenes in this distance to COM. How do I obtain this fraction in this distance by RDF, Please? Thank you again. Best Regards Dina -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] the radius of dry core

Dear GROMACS Specialists, I am working about micelles and have a question about the radius of dry core. May I ask you to answer me, Please? In one paper, I saw that the radius of dry core equals where the density profiles of water and the surfactant hydrocarbon tails cross and a fraction of

[gmx-users] the radius of gyration

Dear Gromacs Specialists, I ran one micelle system and obtained the radius of gyration for this as follows: (g_analyze -f gyrate.xvg -av -ee)    standard   -   cumulants from those of set  average   deviation  sqrt(n-1)   a Gaussian distribition  

[gmx-users] Clustering

Hi Erik, Thank you very much from your response. Best Regards Dina From: Erik Marklund er...@xray.bmc.uu.se To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, April 16, 2012 12:07 PM Subject: Re: [gmx

[gmx-users] Clustering

Dear GROMACS Specialists, May I know about clustering, Please? I want cluster small organic molecules. Is it possible? They collected in some places together and they are separate in the other place. Please help me. Thank you very much in advance. Best Regards Dina-- gmx-users mailing list

[gmx-users] Clustering

From: Erik Marklund er...@xray.bmc.uu.se To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, April 15, 2012 12:58 PM Subject: Re: [gmx-users] Clustering Try g_clustsize Erik 15 apr 2012 kl. 09.00 skrev dina dusti: Dear GROMACS

[gmx-users] martini coarse-grained

Dear GROMACS Specialists, I have doubt about definition of tiofen ring in MARTINI CG force field. May I ask you to help me, Please? I defined if as: SC4 and SC5, that SC5 is as S-C-C and SC4 is as C-C. Is it right? Or should I change SC5 to C-S-C for .gro file? And my definition of tiofen in

[gmx-users] martini coarse-grained

- Forwarded Message - From: dina dusti dinadu...@yahoo.com To: XAvier Periole x.peri...@rug.nl Sent: Tuesday, April 10, 2012 10:44 PM Subject: martini coarse-grained Thank you very much from your response. I found the coordinate file of tiofen from PRODRG and I wrote .itp file

[gmx-users] martini coarse-grained

, they become similar together!!! Please help me. Thank you very much again. Best Regards Dina From: Tsjerk Wassenaar tsje...@gmail.com To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, April 10, 2012 11:38 PM

[gmx-users] volume in ensemble

Dear GROMACS Specialists, May I ask you to answer my question, Please? I  have several systems consist of water and different molecules (surfactant and etc. with same molecule number in all of them except water)  that equilibrated them in NPT ensemble, I wanted to have all of systems with same

[gmx-users] volume in ensemble

Dear Tsjerk, Thank you very much from your response. How do I consider this in my analysis, Please? Best Regards Dina From: Tsjerk Wassenaar tsje...@gmail.com To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent

[gmx-users] pdb file

Dear Oliver, Thank you very much from your help. Excuse me for delay to thank you because I saw your mail now! Best Regards Dina From: Oliver Stueker ostue...@gmail.com To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users

[gmx-users] pdb file

Dear Gromacs Specialists, I need pdb file of tiofen, but I didn't find it!!! Can I change pdb file of one compound that is as same as tiofen (for example pyrrole) and give it to PRODRG for obtain gro file and topology file of tiofen? Please help me. Thanks in advance. Best Regards Dina --

[gmx-users] pdb file

Thank you very much from your response. Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, March 12, 2012 10:02 PM Subject: Re: [gmx-users] pdb

[gmx-users] Martini

Dear Gromacs Specialists, May I ask you to help me for definition of pyrrole, tiofen and aniline in MARTINI coarse-grained force field, Please? I defined them as following: aniline (one benzene ring+NH2) = SC4, SC4, SNd pyrrole (one aromatic ring consists of 4 carbon and one NH) = SC4, SP1

[gmx-users] Martini

I know your cause for this definition, Please? Best Regards Dina From: Dariush Mohammadyani d.mohammady...@gmail.com To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, March 8, 2012 11:24 PM Subject: Re

Re: [gmx-users] Martini

Thank you very much from your response. Best Regards Dina From: Dariush Mohammadyani d.mohammady...@gmail.com To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, March 9, 2012 1:05 AM Subject: Re: [gmx

[gmx-users] g_fg2cg

Dear Andrzej, I checked all of files and there is no problem in them. I before did it (g_fg2cg) for one surfactant and was performed correctly. I want to calculate the center of mass of atoms in one bead manually (each CG bead is at the center of mass of the FG atoms that map to it) for cg.gro,

[gmx-users] g_fg2cg

Dear Gromacs Specialists, I have one problem about g_fg2cg. I want convert structure of butanole in fg to cg by g_fg2cg, but I take this error: Program g_fg2cg, VERSION 3.3.1 Source code file: gmxfio.c, line: 735 Range checking error: Variable fio has value -1. It should have been within [ 0

[gmx-users] g_fg2cg

Dear XAvier Thank you very much from your response. Yes, I defined mapping in atomistic topology as: [mapping ]   1   1    2    3    4    5  6 because for butanole we have one bead. Please help me. Best Regards Dina -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] error

Dear Mark, Thank you very much from your response. May I ask you to tell me what is about time scale of convergence for radius of gyration, momentum and radial distribution function (rdf) in fine-grained and coarse-grained, Please? (autocorrelation time)  As same as that you told me Different

[gmx-users] error

Dear Gromacs Specialists, My total time for simulation is 60 ps (600 ns) because I work with MARTINI coarse-grained force field and this time is enough for my system, but when I do g_analyze -ee, I take this warning:  Warning: tau2 is longer than the length of the data (864000) the

[gmx-users] error

Dear Mark, Thank you very much from your response. Can you tell me what is the best solution for this warning, Please? Warning: tau2 is longer than the length of the data (864000) the statistics might be bad In addition to this warning is related to error estimate for radius of gyration and

[gmx-users] g_analyze -ee

Dear Gromacs Specialists, I have one problem about g_analyze -ee, May I ask you to help me, Please? When I do this program as g_analyze -f .xvg -av -ee, it is as followed: Read 4 sets of 83001 points, dt = 6   std. dev.    relative deviation of    

[gmx-users] g_analyze -ee

for thank from you. Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, February 18, 2012 5:29 PM Subject: Re: [gmx-users] g_analyze -ee dina dusti

[gmx-users] g_analyze -ee

Dear Justin, Thank you very much from your response. Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, February 20, 2012 11:07 PM Subject: Re

[gmx-users] g_analyze -ee

Dear Gromacs Specialists, Sometimes, when I do g_analyze -f  .xvg -av -ee error.xvg , I take following warning, and I don't know how to fix it. Set   1:  err.est. 0.000596502  a 0.29217  tau1 24.8856  tau2 443.641 Warning: tau2 is longer than the length of the data (864000) the

[gmx-users] error estimate

Dear Prof. I computed the total radius gyration and the radius of gyration in x, y and z directions that all of them are into one file named gyrate.xvg. Then I want to calculate error estimate for all of them separately. I do as: g_analyze -f gyrate.xvg -ee error.xvg and is printed on

[gmx-users] g_dist

. Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, February 2, 2012 12:08 AM Subject: Re: [gmx-users] g_dist dina dusti wrote: Dear Prof

[gmx-users] g_dist

Dear Prof. Thank you very much from your response. Yes, I contacted with one of them and she said me use g_dist, but I have problem with it. Thank you again because of your patient. Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti

[gmx-users] g_dist

micelle and for example head group and then used g_analyze for dist.xvg and I had the quantity near zero!!! Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org

[gmx-users] g_dist

Dear Prof. Thank you very much from your help. Best Regards Dina -- 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

[gmx-users] g_dist

Dear Prof. Thank you very much from your help. Best Regards Dina -- On 3/02/2012 3:17 AM, dina dusti wrote: Dear Prof Thank you very much

[gmx-users] g_dist

...!!! Where is my mistake? I select groups in index file correctly. Please help me. Thank you again. Best Regards Dina  From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent

[gmx-users] g_dist

Dear Prof. Thank you very much from your response. I removed pbc and jump in my system, and when I see my system as visual in ngmx, there is not pbc and jump and has been created one micelle and it remain stable for long times. I really don't know what should I do! Best Regards Dina --

[gmx-users] g_dist

. Perhaps I am wrong about required program (command) for calculation of root-mean-square distance? Please help me. Thank you again. Best Regards Dina  From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users

[gmx-users] g_dist

Dear Prof. Thank you very much from your response. He answer me that I should use from g_gyration for radius of micelle, but what should I do for hydrocarbon (dry) core or calculation of inner core of micelle (i.e. the first of carbon on tail of surfactant with COM of micelle)? Best Regards

[gmx-users] g_dist

Dear Gromacs specialists, Can you help me about g_dist? I have a micelle system, I want to obtain distance between center of mass of micelle with the last of carbon bounded to head group in surfactant. It should be near 2.2 but when I did   g_dist -f md.xtc -s md.tpr -b 15 -o dist.xvg and

[gmx-users] g_dist

Dear Prof. Thank you very much from your response. Yes, dist.xvg has four column consists origin distance and distances in direction x, y , z. So distance that I want according to result of g_analyze, is 5.324286e-02 that isn't correct. I selected 2 groups, micelle and the last carbon

Re: [gmx-users] root-mean-square distance

of the headgroup atoms from the micelle center of mass. May I ask you to help me? Best Regards Dina From: Tsjerk Wassenaar tsje...@gmail.com To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, January 29, 2012

Re: [gmx-users] root-mean-square distance

, but it dose not have anything to determine center of mass of micelle.  Best Regards Dina From: Tsjerk Wassenaar tsje...@gmail.com To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, January 29, 2012 11:26

[gmx-users] root-mean-square distance

Dear Specialists, I have a problem about computing of radius of micelle by root-mean-square-distance. Please help me. I obtained radius of my micelle 2.4 nm by g_gyrate. g_gyrate -f md.xtc -s md.tpr -o gyrate.xvg -b 15 I want compare it by rms distance. I use from g_rms as following:

[gmx-users] micelle formation

Dear Specialists, I am a beginner in grmacs and I have several questions about formation of micelle in gromacs. Please help me. 1- We know that there is a thermodynamic equilibrium between created micelle and free monomers in solvent, but I don't see this in results of my simulation! When I

[gmx-users] micelle formation

Dear Prof. Thank you very much from your reply. My question about R(micelle)=(1.291)R(gyration) is that, what is cause of coefficient 1.29? Yes, I saw one micelle that the tails of surfactants are into the micelle and heads are out of micelle visually (consist of 80 monomer). My results that

[gmx-users] (no subject)

-- 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)subscribe requests to the list. Use the www interface or send it to

[gmx-users] (no subject)

-- 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)subscribe requests to the list. Use the www interface or send it to