[gmx-users] Requiring to post message

Dear Administrator, My e-mail is s1460...@st.kmutt.ac.th Best regards, Patcharida Kaewmanee -- 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! P

[gmx-users] Re: g_bundle -na option for calculating angle between helices

anyone ? :) On Fri, Jul 22, 2011 at 1:19 PM, maria goranovic wrote: > Hi > > I am trying to calculate angle between helices using g_bundle and: > > http://lists.gromacs.org/pipermail/gmx-users/2007-October/030415.html > > I >

[gmx-users] polt of eigenvector change for a residue

Dear users how can i have the plot whitch shows a perticular eigenvalue changes, for my protein residues? regards, sajad-- 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

Re: [gmx-users] Micelle Modeling

I used your tutorial but am getting the error message WARNING 1 [file dpc.top, line 28]: 18915 non-matching atom names atom names from dpc.top will be used atom names from dpc.gro will be ignore probably because my .top file was generated using a file generated thru PRODRG (only inputing 23

Re: [gmx-users] Micelle Modeling

Janowicz, Adrianna C. wrote: I used your tutorial but am getting the error message WARNING 1 [file dpc.top, line 28]: 18915 non-matching atom names atom names from dpc.top will be used atom names from dpc.gro will be ignore probably because my .top file was generated using a file genera

[gmx-users] PostDoc position in molecular biomechanics of coagulation proteins

Please excuse the spam if you are not interested in a post doc position. Otherwise, please read on ... PostDoc Position in the Molecular Biomechanics group at the Heidelberg Institute for Theoretical Studies (HITS) in Heidelberg, Germany We are seeking a highly motivated candidate for a postdo

[gmx-users] Single long simulation versus multiple short ones

Dear gromacs user, I have been trying to look for an answer for my following question from our forum but still couldn't manage to find one. Probably it is trivial but I am not sure. Instead of running a single relatively long simulation (say for about 30 ns), is it acceptable if we simulate multi

Re: [gmx-users] Single long simulation versus multiple short ones

Widya Desmarani wrote: Dear gromacs user, I have been trying to look for an answer for my following question from our forum but still couldn't manage to find one. Probably it is trivial but I am not sure. Instead of running a single relatively long simulation (say for about 30 ns), is it

Re: [gmx-users] Single long simulation versus multiple short ones

Hey Widya, In general, no, 15*2ns is not equal to 1*30ns. The reason for this lies in correlation and relaxation times. 15 simulations of 2ns give good statistics on relaxation and, if the system is equilibrated already, on short-term processes. A single simulation of 30 ns may relax to equilibriu

[gmx-users] water box size from output files

Hi I was wondering if there is a way to determine the water box size from the output files after the simulation run is over Thanks Rabab Toubar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromac

Re: [gmx-users] water box size from output files

Rabab Toubar wrote: Hi I was wondering if there is a way to determine the water box size from the output files after the simulation run is over Box vectors are printed to the output coordinate file (final snapshot) and can be extracted from along the trajectory from the .edr file. -Just

[gmx-users] How to read XTC file in fortran code

Hi, I was planning to do some analysis by reading in a XTC file using Fortran code . I was wondering what is the best possible option I can have . Sanku-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.

Re: [gmx-users] How to read XTC file in fortran code

Sanku M wrote: Hi, I was planning to do some analysis by reading in a XTC file using Fortran code . I was wondering what is the best possible option I can have . Start here: http://www.gromacs.org/Documentation/How-tos/Reading_XTC_From_Fortran Then search the archives; this topic has been

Re: [gmx-users] water box size from output files

Thanks Justin for your reply. But what is the extension of the output coordinate file. And for the .edr file it failed to open in windows; how can I possibly view it Thanks Rabab Toubar --- On Mon, 7/25/11, Justin A. Lemkul wrote: > From: Justin A. Lemkul > Subject: Re: [gmx-users] water b

[gmx-users] use of SW.itp...

Dear All: I am trying to make use of polarizable water models. I have attempted to employ the Maaren & van der Spoel [2001. JPC 105:2618] model embodied by the sw.itp embedded in share/gromacs/top. I encountered the following issues: 1. the lines: ; [ defaults ] ; LJGeometric where

[gmx-users] genbox -shell

Hi All, I have a question about genbox -shell option. The online manual says: *-shell* real 0 thickness of optional water layer around solute The value specified for -shell option, example 3, produces a sphere with radius 3 nm or diameter 3 nm? Thanks, SN -- gmx-users mailing listgmx-us

Re: [gmx-users] water box size from output files

rabab, justin mentioned the *gro file saved at the end of the simulation - the last line contains the box dimensions. you can extract them with g_energy: g_energy -f your_edr_file -o your_output_file and then selecting: Box-X Box-Y Box-Z good luck, igor Igor Marques On Mon, Jul 25, 201

Re: [gmx-users] genbox -shell

shivangi nangia wrote: Hi All, I have a question about genbox -shell option. The online manual says: *-shell*real0 thickness of optional water layer around solute The value specified for -shell option, example 3, produces a sphere with radius 3 nm or diameter 3 nm?

[gmx-users] g_velacc

Hello, I am calculating the velocity autocorrelation function for my system. I have to calculate the g_velacc for 5 different groups within system. I have made the index file. I have also written .sh script g_velacc -f 6.trr -s 6.tpr -n glu-emi-dmp-128-no.ndx -nonormalize -o h20-vac.xvg 24 g_

Re: [gmx-users] g_velacc

Nilesh Dhumal wrote: Hello, I am calculating the velocity autocorrelation function for my system. I have to calculate the g_velacc for 5 different groups within system. I have made the index file. I have also written .sh script g_velacc -f 6.trr -s 6.tpr -n glu-emi-dmp-128-no.ndx -nonormal

[gmx-users] Re:g_velacc

> > I am calculating the velocity autocorrelation function for my > system. I have to calculate the g_velacc for 5 different groups within > system. I have  made the index file. > > I have also written .sh script > >  g_velacc -f 6.trr -s 6.tpr -n glu-emi-dmp-128-no.ndx -nonormalize -o > h20-vac.xv

[gmx-users] Use of non-standard CHARMM27 forcefield in Gromacs - how?

Dear all, During my PHD studies we developed a specific lipid force field based on the CHARMM27 force field containing spingomyelin molecules of various saturation and chain lengths. Now I would like to use this forcefield in Gromacs but I don't know where to start. Is there a way to import it i

Re: [gmx-users] Use of non-standard CHARMM27 forcefield in Gromacs - how?

Jernej Zidar wrote: Dear all, During my PHD studies we developed a specific lipid force field based on the CHARMM27 force field containing spingomyelin molecules of various saturation and chain lengths. Now I would like to use this forcefield in Gromacs but I don't know where to start. Is th

[gmx-users] multiple protein interaction

hi all, I am new to GROMACS.I would like to know how we will simulate putting more than two or more molecules of same proteins inside the box and do simulation?Is there any possibility to replace 100 atoms or so of solvent with proteins? Please help. Regards, smriti -- gmx-users mailing listg

[gmx-users] OPLS for group -N=CH2

Dear users. Help me. What parametres of force field OPLS it is necessary to be used for group -N=CH2 (imine group) ? The best regards, Igor -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org