Re: [gmx-users] How to use deuterium order parameters

On Wed, Nov 2, 2011 at 2:06 PM, Alex wrote: > Dear All > > I'd like to perfom a deuterium oerder parameters analysys in a system with > DPPC > + Protein + Water > I read that I've to make an index file that contains one group each for > every > carbon atom in the acyl-chain (starting > with the c

Re: [gmx-users] lipid membrane slicing

to analyse each trajcetory and get the order parameters for each group of lipids. good luck, igor Igor Marques On Tue, Oct 11, 2011 at 6:20 PM, Poojari, Chetan wrote: > Hi, > > I have protein completely inserted into lipid membrane and would like to > study order parameter

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

Re: [gmx-users] Calculation of unsaturated deuterium order parameters for POPC

> in that index doing this, for C9 and C10 i've obtained the following values 0.0738068 -0.000533683 that you should then replace in the correct positions in the sn2 output good luck, and sorry if i'm missing the point :| igor Igor Marqu

Re: [gmx-users] electron density

thanks mate! Igor Marques On Thu, May 26, 2011 at 6:12 PM, Justin A. Lemkul wrote: > > > Igor Marques wrote: > >> dear all, >> >> regarding the matter of electron density, can anyone clarify me on the >> output units? >> from this discussio

Re: [gmx-users] electron density

dear all, regarding the matter of electron density, can anyone clarify me on the output units? from this discussion i understand the values are presented in electrons/A^3 - is this correct? best regards, igor Igor Marques Molecular Modeling Group – Univ. of Aveiro http://molecular

Re: [gmx-users] g_order output is mirrored

hain in the index files? although that makes the plot resemble the ones already published, i don't think that is the definitive solution to this problem! (this applies also to the DMPC chains of my colleague) best regards! igor Igor Marques On Tue, May 17, 2011 at 9:47 PM, Ig

Re: [gmx-users] g_order output is mirrored

Igor Marques On Tue, May 17, 2011 at 9:42 PM, Justin A. Lemkul wrote: > > > Igor Marques wrote: > > > > > 2. Can you post your .ndx file? >>for sn1 chain: >> >> Reading structure file >> Going to read 1 old index file(s) >>

Re: [gmx-users] g_order output is mirrored

Igor Marques On Tue, May 17, 2011 at 8:04 PM, Justin A. Lemkul wrote: > > > Igor Marques wrote: > >> dear all, >> >> i've been trying to use g_order to analyse the disorder of the chains of >> POPC model membrane simulations, namely the SCD

[gmx-users] g_order output is mirrored

: g_order -f ../TRAJECTORY.xtc -s ../TOPOLOGY.tpr -n INDEX_CHAIN_sn1.ndx -od OUTPUT_SCD.xvg what are we not doing/doing wrong? best regards and thanks in advance! Igor Marques <>-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

Re: [gmx-users] g_membed tool

this manual<http://wwwuser.gwdg.de/%7Eggroenh/submitted/Membed_rev.pdf>, that apparently compiles both the page and the article. good luck, Igor Marques On Wed, Mar 16, 2011 at 4:51 AM, Mohana lakshmi wrote: > Dear all.. > > I am using g_membed tools to embed the protein

Re: [gmx-users] creating a bilayer of dppc

dear delara, converting the monolayer gro to pdb with editconf and then using that pdb in packmol might be a way of doing it. don't forget to adjust your *top file to the new number of items (2x) and their order. that should do it, i guess best regards, igor Igor Marques

[gmx-users] neutral plasma

Hello everybody, I've digging around the user manual, the website and the mailing list archives and I'm afraid I might be missing something: does GROMACS have some kind of *neutral plasma *as AMBER does? Or every simulation must have a net charge of 0.000 ? Best regards, Ig