[gmx-users] RE: Position restraints

Thank you for responce and explanation! So is it a good alghorithm to use gromacs genrestr command and then include this posre.itp file into topology (without any changes) after insertion of a ligand.itp? Thank you in advance On 4/2/13 6:07 AM, alex rayevsky wrote: Dear All! I have a doubt

[gmx-users] Position restraints

Dear All! I have a doubt about the rightness of ligand/molecule integration in the topology file. I'm using an amber (tleap) or swissparam.ch to build a topology of the residue (modified trna). Is it neccessary to generate a position restrain file (genrestr program) for this residue or not? I've st

[gmx-users] correct usage of freezing group

Hi dear All! Good day dear forum! I have a question abour freezing of atoms during MD. The idea is that - I have a protein and one domain contains a site. Also I have two ligands, one of them is better inhibitor in comparison with another one. To prepare the topology of the inhibitor I need to use

Re: [gmx-users] Freeze group atoms changing position

Just as an update, I ran the simulation using position restraints with force constants set to 1 for each atom in the restrained waters, and none jumped out of the nanotube. Thanks for the help! On Thu, Nov 1, 2012 at 5:01 PM, Justin Lemkul wrote: > > > On 11/1/12 4:56 PM, Alex

Re: [gmx-users] Freeze group atoms changing position

ng out of bounds. Is it actually possible to only apply position restraints to some molecules within a species and leave the rest alone? On Wed, Oct 31, 2012 at 3:57 PM, Justin Lemkul wrote: > > > On 10/31/12 3:55 PM, Alex Marshall wrote: > >> Chris, is that for freeze groups

Re: [gmx-users] Freeze group atoms changing position

hey're identified with the appropriate topology > file. Does this sound like it would work? Is there some other way that you > might do it? > > Thanks > > On Fri, Oct 26, 2012 at 5:18 PM, Alex Marshall wrote: > > > Justin: I'll try using position r

Re: [gmx-users] Freeze group atoms changing position

oms I want to freeze so that they're identified with the appropriate topology file. Does this sound like it would work? Is there some other way that you might do it? Thanks On Fri, Oct 26, 2012 at 5:18 PM, Alex Marshall wrote: > Justin: I'll try using position restraints instead of

Re: [gmx-users] Freeze group atoms changing position

me two waters have jumped. I'll check the manual again though. Thanks. On Thu, Oct 25, 2012 at 10:43 AM, Bogdan Costescu wrote: > On Thu, Oct 25, 2012 at 3:59 PM, Alex Marshall wrote: > > Thanks Justin. I identified the offending waters using vmd (adding 1 to > > resID and at

Re: [gmx-users] Freeze group atoms changing position

24, 2012 at 9:22 PM, Justin Lemkul wrote: > > > On 10/24/12 3:17 PM, Alex Marshall wrote: > >> Hi all, >> >> I'm simulating a system of two reservoirs connected by a carbon nanotube. >> The reservoir wall atoms and carbon nanotube atoms are held in place

[gmx-users] Freeze group atoms changing position

but after 20 ns two of the frozen water molecules have jumped outside of the nanotube into a supposedly inaccessible region. What could cause this? Should I be worried? -- Thanks, Alex Marshall M.Sc -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo

Re: [gmx-users] How to create two parallel wall?

rch 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-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailin

Re: [gmx-users] Re: Measuring hydrogen bonding in a specific region

are allowed! > * 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-requ...@gromacs.org. > * Can't post? Read http://ww

[gmx-users] Measuring hydrogen bonding in a specific region

each reservoir Is there any way I could automate/improve this process? I have ten of these simulations longer than 100 ns to analyze, and I just need more data points than I can crank out manually. Thanks. -- Alex Marshall M.Sc. Candidate Department of Applied Mathematics The University of Western

Re: [gmx-users] "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group" error during minimization with TPO residue

I apologize to anyone who wasted their time reading my original post: I found that integrator had been misspelt in the em.mdp file, causing it to default to integrator = md. After fixing the mistake, no more errors resulted. Alex On Tue, Jun 5, 2012 at 4:46 PM, Justin A. Lemkul wrote: > >

[gmx-users] "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group" error during minimization with TPO residue

found in the gromos43a1p directory because of previously discussed issues with the format. I also added the ions.itp, spce.itp, and ff_dum.itp to the directory. However, after inputting the same commands and using the single TPO residue, I received the same error. Alex Cumberworth Log file opened

Re: [gmx-users] Velocities in trjconv 4.5.5

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 > -- Alex Marshall M.Sc. Candidate Department of Applied Mathematics The University of Western Ontario -- gmx-users mailing listgmx-use

[gmx-users] Minimization Problems

hem approaching inf. Can anyone find anything glaringly wrong with my .mdp? Thanks, Alex Seling title = Minimization of alpha-synuclein cpp = /lib/cpp -traditional define = -DFLEXIBLE integrator = sd constraints = none tinit = 0 dt = 0.001 nsteps = 100 emtol = 0.1 emstep = 0.1 nstcgsteep = 1

Re: [gmx-users] can mdrun append output files without the proper .cpt?

Thanks Mark! On Tue, Jan 31, 2012 at 7:26 PM, Mark Abraham wrote: > On 28/01/2012 7:09 AM, Alex Marshall wrote: > > Hi all, > I was trying to extend my simulation but I used the wrong .tpr file when I > called mdrun_mpi. I didn't catch it in time and my checkpoint files wer

[gmx-users] can mdrun append output files without the proper .cpt?

imulations), but when I use mdrun_mpi -append with the extended .tpr file, new output files are generated anyway. Is there a way around this, or will I just have to use trjcat or something once the new run has finished? Thanks. -- Alex Marshall M.Sc. Candidate Department of Applied Mathematics The

Re: [gmx-users] System Exploding

Given the unfavorable input, then, it seems odd then that the same .mdp and protein ran consistently on 4.0.7, and I can't seem to find anything in the changelog to indicate a relevant change. On Thu, Jan 26, 2012 at 1:26 AM, Mark Abraham wrote: > On 26/01/2012 5:10 PM, Alex Seli

[gmx-users] System Exploding

quot; for a few interactions, with each of them approaching inf. This is with a good starting configuration. Any ideas as to the error? My .mdp file is below. Thanks, Alex Seling title = lea at 300K cpp = /lib/cpp -traditional integrator = md ;sd ;md ;bd tinit = 0.0 dt = 0.001 ;time step of 1 fs nsteps

[gmx-users] Help with Principal component analysis

Dear all   I run a MD on a GPCR (transmembrane protein) Then I run a PCA on results and I found 3PC sufficient to explain variance. On the same PC I get big values for samples located both at Nter (extracellular) and Cter (intracellular) or for similar cases such as both Nter(extracellular) and L

[gmx-users] Help with g_density

Dear All I run g_density on a membrane protein. Here are the results   http://elisacarli.altervista.org/densityhead.jpg http://elisacarli.altervista.org/tailsDensity.jpg   Could you help me to give an interpretation to my analysis?   Thank in advance-- gmx-users mailing listgmx-users@gromacs.

[gmx-users] Information about boxX,boxY e boxZ

Dear All   I run a 1ns MD on a membrane protein and I get these values for box coordinate's Energy  Average   Err.Est.   RMSD  Tot-Drift --- Box-X    13.867  0.071   0.167634 

[gmx-users] Information about g_sas

Dear all   Which is the difference between hydropilic and hydrophobic sas? How can give an interpretation to g_sas xvg graph? What can I find out in it and how can use g_sas to analyze a trajectory?   Thanks-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinf

[gmx-users] Convert xpm to matrix

Dear all,   I'd like to convert an xpm file to delimited CSV , because I need to import values in excel.   Any suggestion?   Thanks-- 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/Ma

[gmx-users] Cluster analysis

Dear all   Could you give me any suggestion about how I can interpretate output result of g_cluster? Is there a detailed tutorial?   Thanks-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Su

[gmx-users] Convert to Sammon map

Dear All   I'd like to convert a gromacs RSMD matrix (xmp) to a Sammon map. Could you give me any suggestion?   Thanks-- 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/Se

[gmx-users] NVT Equilibration

Dear all I'm studying a membrane protein. I've run equilibration with the follwing parameters - reference temperature =323k integrator = md ; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs tcoupl = V-rescale ; modified Berendsen thermostat The syst

[gmx-users] NVT Equilibration

Dear all I'm studying a membrane protein. I've run equilibration with the follwing parameters - reference temperature =323k integrator = md  ; leap-frog integrator nsteps  = 5  ; 2 * 5 = 100 ps dt  = 0.002  ; 2 fs tcoupl  = V-rescale ; modified Berendsen thermostat The syst

[gmx-users] Cavity detection on membrane protein surface

Dear all, I'm studying a membrane protein. During MD some concavities appear and disappear on its surface. I'd like to isolate atoms and residues involved in these formations. Any suggestion? Which steps should I follow to automate the identification process?   Thanks in adavance-- gmx-users mai

Re: [gmx-users] Trajectory to matrix

  Where can I download the old version? Thanks Da: Mark Abraham A: Discussion list for GROMACS users Inviato: Martedì 22 Novembre 2011 9:32 Oggetto: Re: [gmx-users] Trajectory to matrix On 22/11/2011 7:27 PM, Alex Jemulin wrote: Dear all >I need to exp

[gmx-users] do_dssp segmentation fault

Dear all I'm experiencing the following error in Gromacs 4.5 with do_dssp Here is the command do_dssp -f md.xtc -s md.tpr -o secondary-structure.xpm -sc secondary-structure.xvg -dt 10 give me the following error segmentation fault How can I fix it? Thank in ad-- gmx-users mailing listgmx-

[gmx-users] Trajectory to matrix

Dear all I need to export all MD trajectory's data to a matrix. As column header I'd like to put each atom indentified by residue name and progressive number e.g. LYS-N1 In the rows I'd like to put z coordinate changing in time.   Any  suggestion?   Thanks-- gmx-users mailing listgmx-users@gr

[gmx-users] Problems with g_filter

Dear all I'm trying to use the follow command with a protein in DPPC and explicit water   g_filter -s md.tpr -f md.xtc -ol movie_filtered.pdb -fit -nf 5   Altough I selected protein group, the command export everything (water + protein + dppc).   How can I fix it?   Thanks in advance-- gmx-users

[gmx-users] Extract van der waals surface atoms coordinates

Dear All   How can I extract van der waals surface atoms coordinates from MD Trajectory and write them to a file? Is it possible with gromacs? And with other tools? Any suggestion?   Thanks in advance-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-

[gmx-users] Gromacs 3D maps

Dear all, I'd like to transform an md gromacs trajectory in a 3d maps set. I mean that every 100ps, I need to export frame coordinates to a 3d map. Than I need to compare a map with the following. Could give me any advice about tools/software to use? Additionally I need to export the coordinate (

[gmx-users] Remove water from membrane protein

Dear all, I've inserted a protein in a DPPC layer and then I've solvated (after modifying vdwradii.dat to avoid putting waters in wrong places). How can I check and eventually remove waters still being in wrong places? I've tried to load it in PdbViewer and in rasmol, but is veruy difficult to di

Re: [gmx-users] A question about deuteriu order parameters graph

c -n sn2.ndx -d z -od deuter_sn2.xvg Thank your very much for your support Bests Da: Javier Cerezo A: gmx-users@gromacs.org Inviato: Martedì 8 Novembre 2011 9:45 Oggetto: Re: [gmx-users] A question about deuteriu order parameters graph Hi Alex Deuterium order pa

[gmx-users] A question about deuteriu order parameters graph

Dear All, I run a MD simulation on a membrane protein using DPPC and I performed a deuterium order parameters on the trajectory. As I'm a newbie, could you kindly help me to give an interpretation of these graphs? You can open them at: sn1 http://www.freeimagehosting.net/137c9 sn2 http://www.f

[gmx-users] Sorry for posting twice

I'm sorry for having post the message about deuterium twice. It ws a mistake -- 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] Problems with deuterium graphs

Dear All, I run a MD simulation on a membrane protein using DPPC and I performed a deuterium order parameters on the trajectory. As I'm a newbie, could you kindly help me to give an interpretation of these graphs? You can open them at: sn1 http://www.freeimagehosting.net/137c9 sn2 http://www.f

[gmx-users] How to use deuterium order parameters

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 carbonyl-carbon and going further down). Where can I get carbo

[gmx-users] g_analyze errors

Dear all, I run a NPT equilibration (1 ns - 1000 steps) and then I drew pressure graph using g_energy. I've tried to run the following command g_analyze -f pressure.xvg -av average.xvg -ee errest.xvg G_ANALYZE PRESSURE*** But I get the following output Read 1 s

Re: [gmx-users] Dimensionless units question

ribution then LJ parameters should also be > correct and for that you should switch to standard gromacs units. > > Also why do you need to use gmx.ff, seems to me that you already have the > parameters (ie the LJ parameters and charges) > > > On Fri, Jul 29, 2011 at 11:30 AM, A

Re: [gmx-users] Dimensionless units question

hink I can simply compare their ratios, as there would still be a unit of length to deal with. Thanks, Alex On Fri, Jul 29, 2011 at 2:24 PM, Amit Choubey wrote: > Hi, > > reduced units works for LJ particles only. I am not sure if it works when > you include electrostatics. When yo

[gmx-users] Dimensionless units question

are still quite far from the reference values. Have I missed anything if I want my output to be in dimensionless units? Thanks, Alex -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Suppor

[gmx-users] Re: Polarizable water model

f them has fluctuating charge or dipole so no electronic polarization is simulated, isn't it? -- Alex [comcon1] Nesterenko, PhDer of biophysical department, Biology Faculty. MSU. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

[gmx-users] Polarizable water model

models? Thanks beforehand! -- Alex [comcon1] Nesterenko, PhDer of biophysical department, Biology Faculty. MSU. -- 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

[gmx-users] Slab Ewald test

0 0 ; qtot 0 23 H 12 CHR H3 23 1 1 H 0 0 ; qtot 0 24 H 12 CHR H6 24 -1 1 H 0 0 ; qtot 0 25 H 13 CHR H3 25 1 1 H 0 0 ; qtot 0 26 H 13 CHR H6 26 -1 1 H 0 0 ; qtot 0 Thanks, Alex Marshall -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

Re: [gmx-users] How to control and interpret g_density analysis more precisely?

Thanks. Do you mean the "-d" option? What exactly does it mean by "take the normal on the membrane"? What membrane? What if I was simulating a system that doesn't have any membranes? Thank you, Alex On Fri, Aug 27, 2010 at 5:55 PM, Justin A. Lemkul wrote: &

[gmx-users] How to control and interpret g_density analysis more precisely?

erstanding and control over what exactly g_density is doing because right now I feel that I'm just getting some numbers out but who knows how. Thanks! Alex -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://

[gmx-users] question about how to jump into an archived discussion...

send the person an email, then it will just become a personal email correspondence between myself and that person, right?? Then it won't be added to the web-based archive as a new post. How can I jump into the discussion and add my question/comment to the existing posts?? Thanks a lot, Alex -

Re: [gmx-users] Lipid topologies, carving, etc

I see. Well, maybe doing the old school manual carving isn't a bad idea, after all. I still think your script is extremely useful, will definitely write to you if I need it. Thanks, Alex On Thu, May 6, 2010 at 1:44 AM, Kukol, Andreas wrote: > Alex, > > I used the membrane bu

[gmx-users] Lipid topologies, carving, etc

o, is there any software other than the inflategro script and g_membed that helps automate the protein-lipid assembly? Thanks a bunch, Alex -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.or

Re: [gmx-users] POPC 53a6 topology (dihedral multiplicity)

Thanks Andreas. Is there any difference force-wise between this and our little workaround? Alex On Mon, May 3, 2010 at 2:17 PM, Kukol, Andreas wrote: > Hi, > > The POPC_53a6 topology works only with Gromacs versions lower than 4. > Please find attached the topology compatible w

Re: [gmx-users] POPC 53a6 topology (dihedral multiplicity)

, 2010 at 10:57 AM, XAvier Periole wrote: > > HAve look at the paper describing the topology ... > > > On May 3, 2010, at 6:52 PM, Alex Smolyanitsky wrote: > > Hello everyone, > > I am trying to include a POPC 53a6 topology from LipidsForGro96_53a6.zip ( > http://w

[gmx-users] POPC 53a6 topology (dihedral multiplicity)

be set according to the older topology? I know similar questions have been asked here in the past, but I really want to make sure my topology is sane. Thanks a lot. Alex -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at htt

Re: [gmx-users] Isovaline vs Valine

Ahhh, thanks. I was one of the sort "It's in front of your nose, dear!!""" Alex David van der Spoel <[EMAIL PROTECTED]> wrote: Alex Simperler wrote: > Dear Gromacs Users! > I have Isovaline in my Protein. It is not supported in the > aminoacids.da

[gmx-users] Isovaline vs Valine

Dear Gromacs Users! I have Isovaline in my Protein. It is not supported in the aminoacids.dat file. Can I simply call it VAL for the calculations or do I need to insert the data by hand. Is there any routine described online that tells me what I have to change? Regards Alex

[gmx-users] mesoscopic Bose condensation (mBC) in water and biosystems

this problem real and interesting, as a new quantum factor of biopolymers folding (still missing in theory of biosystems self-organization), please contact me.    Thanks.    Alex Kaivarainen    Dept of Physics, University of Turku, Finland.    [EMAIL PROTECTED]    web.petrsu.ru/~alexk