Re: [gmx-users] membrane protein energy minimization error

Your system is exploding, i.e. you have severe atomic overlap somewhere. Having no idea what you've done to construct your system, it is hard to give any useful advice. It is probably best if you search the list archive for "variable ci" (it will return many useful posts) or search the wiki si

[gmx-users] membrane protein energy minimization error

Dear all Thank you for browsing my question.When I run a K ion channel, I added DOPC bilayer membrane, at the first mdrun, Gromacs program got Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains

[gmx-users] nonequilibrium simulation

Dear GMX users, I would like to simulate non-equilibrium situation and turn off the thermostat along the direction where the external excitation is applied. Could anybody let me know how to do that? Sincerely, Jae H. Park === Jae Hyun Park, Ph.D. Visiting Sch

Re: [gmx-users] Time step in md

On Fri, 2008-09-19 at 20:35 +0400, DimitryASuplatov wrote: > Hello, > could you explain my the secret of choosing to time step for md > integrator? I want to perform a 10-20 ns simulation in water in order > to, for ex., calculate some interactions or to see if the structure > would relax to a stab

[gmx-users] Time step in md

Hello, could you explain my the secret of choosing to time step for md integrator? I want to perform a 10-20 ns simulation in water in order to, for ex., calculate some interactions or to see if the structure would relax to a stable state. If I use vsites, heavyh and LINCS I can run with 6 fs step

Re: [gmx-users] Re: Leaflet of Bilayer

Nicolas Sapay wrote: minnale wrote: Thanks Justin and Nicolas for gave suggestions. I have tried with Nicolas suggested command in VMD Tkconsole, its showing whole popc molecules but not leaflet. I typed the command in Tkconsole like this [atomselect top "name P8 and z>0"] num it has s

Re: [gmx-users] Re: Leaflet of Bilayer

minnale wrote: Thanks Justin and Nicolas for gave suggestions. I have tried with Nicolas suggested command in VMD Tkconsole, its showing whole popc molecules but not leaflet. I typed the command in Tkconsole like this [atomselect top "name P8 and z>0"] num it has showed 201, means the t

[gmx-users] Re: Leaflet of Bilayer

Thanks Justin and Nicolas for gave suggestions. I have tried with Nicolas suggested command in VMD Tkconsole, its showing whole popc molecules but not leaflet. I typed the command in Tkconsole like this [atomselect top "name P8 and z>0"] num it has showed 201, means the total number popc m

[gmx-users] output format of gromacs utilities

Hello, In gromacs analysis tools, is it possible to output multiple data columns as several 'parallel' columns (not as pairs delimited by '&')? I experience difficulties to read such (xvg) format by sigmaplot. -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4

Re: [gmx-users] Peptide aggregation

Dear Dr. Ran Friedman Would you please be so kind to send me your version, to calculate then the rgyr "of the largest aggregate". The box was built with a layer of 1.2 nm around the solute (editconf -d 1.2). Leon Ran Friedman wrote: Dear Leon, You can try to use g_clustsize to get the aggr

Re: [gmx-users] Implicit solvent & PBC

On Fri, 19 Sep 2008 17:25:41 +0200 Berk Hess <[EMAIL PROTECTED]> wrote: From: [EMAIL PROTECTED] Subject: Re: [gmx-users] Implicit solvent & PBC To: gmx-users@gromacs.org Date: Fri, 19 Sep 2008 17:03:08 +0200 On Fri, 19 Sep 2008 16:49:45 +0200 Berk Hess <[EMAIL PROTECTED]> wrote: > > >

Re: [gmx-users] Peptide aggregation

Dear Leon, You can try to use g_clustsize to get the aggregates. I have a version that can calculate the gyration radius of the largest aggregate, but this would work only if your box is big enough and I haven't tried it with rhombic dodecahedron boxes. Ran. Léon Salgado wrote: > Dear gmx users

RE: [gmx-users] Implicit solvent & PBC

> From: [EMAIL PROTECTED] > Subject: Re: [gmx-users] Implicit solvent & PBC > To: gmx-users@gromacs.org > Date: Fri, 19 Sep 2008 17:03:08 +0200 > > On Fri, 19 Sep 2008 16:49:45 +0200 > Berk Hess <[EMAIL PROTECTED]> wrote: > > > > > > > > > >> From: [EMAIL PROTECTED] > >> Subject: Re: [gm

Re: [gmx-users] Leaflet of Bilayer

Justin A. Lemkul wrote: minnale wrote: Hi Jochen thanks for your reply I have gone through this recent mail http://www.gromacs.org/pipermail/gmx-users/2008-September/036508.html more over if I use genconf command like this genconf -f .gro -o out -nbox 2 1 1 -dist 0 0 0 its adding 128 in

[gmx-users] Peptide aggregation

Dear gmx users I did some simulations of multimers (peptides) in rhombic dodecahedron boxes. In the initial configuration of the system, the peptides are close of each other in the center of the box. My aim to see if the peptides do aggregate during the trajectory or if they tend to stay apa

Re: [gmx-users] Implicit solvent & PBC

On Fri, 19 Sep 2008 16:49:45 +0200 Berk Hess <[EMAIL PROTECTED]> wrote: From: [EMAIL PROTECTED] Subject: Re: [gmx-users] Implicit solvent & PBC To: gmx-users@gromacs.org Date: Fri, 19 Sep 2008 16:42:15 +0200 On Fri, 19 Sep 2008 15:00:18 +0200 Berk Hess <[EMAIL PROTECTED]> wrote: > Hi, >

Re: [gmx-users] Re:GROMACS sample procedure

Great! Tsjerk. thanks. -Xianghong Qi On Fri, Sep 19, 2008 at 3:34 AM, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: > Hi, > > The gromacs wiki (wiki.gromacs.org) also lists a number of tutorials, > written from different perspectives. But it doesn't have this one yet :p > > http://nmr.chem.uu.nl/~t

RE: [gmx-users] implicit solvent

Hi, Having a non-uniform dielectric permittivity is a non-trivial problem to solve. I would like to have a solver for such electrostatics in Gromacs, but it is a lot of work to implement (and to make it efficient). Reaction field does not do anything for you in this respect. Berk From: [EMAIL

RE: [gmx-users] Implicit solvent & PBC

> From: [EMAIL PROTECTED] > Subject: Re: [gmx-users] Implicit solvent & PBC > To: gmx-users@gromacs.org > Date: Fri, 19 Sep 2008 16:42:15 +0200 > > On Fri, 19 Sep 2008 15:00:18 +0200 > Berk Hess <[EMAIL PROTECTED]> wrote: > > Hi, > > > > The same as in normal simulations. > > I always use P

Re: [gmx-users] Implicit solvent & PBC

On Fri, 19 Sep 2008 15:00:18 +0200 Berk Hess <[EMAIL PROTECTED]> wrote: Hi, The same as in normal simulations. I always use PME and PBC in my implicit solvent simulations. then - PME: treament of long range electrostatic interactions in implicit solvent? PBC: simulate infinite dilution again i

[gmx-users] implicit solvent

Hi all, I am doing some coarse-grained simulations, where I have removed the solvent molecules from the system. In order to incorporate the effect of solvent in my simulations, I need to tune the dielectric constant of the medium. Will just changing "epsilon_r" in the mdp file work ? Later

[gmx-users] ci range checking error even applying the patch / parallel runs

Hello,after searching extensively the mailing lists I wasn' able to solve my problem. This has to do with running gromacs in parallel (more than one nodes) in a rocks cluster. I 'm able to run a simulation both in one or two processors in a dual core node, yet every time I try to use more than o

Re: [gmx-users] Re[2]: Segmentation fault in Gromacs 4.0 beta1

Thanks so much, Vitaly. Now I will try again. -Xianghong . On Fri, Sep 19, 2008 at 7:58 AM, Vitaly Chaban <[EMAIL PROTECTED]>wrote: > > Hi, > > > > I just noticed that for some time there has been a bug genbox in Gromacs > 4 > > that (always) caused a segv. > > I have fixed it now. > > Berk, > I

Re: [gmx-users] dna-protein simulation

Hi Prasun, Indeed, there's more to the conversion of DNA for gromacs input. Some sed lines: sed -e '{/^.\{13\}H.\'/d; /^.\{13\}H7. THY/d; /^.\{12\}H5''/d}' should get you rid of these hydrogens, and sed -e '{s/\(^.\{13\}C\)7 THY/\15M THY/}' should set the proper name for the DTHY methyl group

[gmx-users] dna-protein simulation

Hello Tsjerk I have solved that problem, now while running PDB2GMX command its giving following error C7 was not found in rtp file so I just compared the atom type in rtp file for DTHY and corresponding pdb file and replace C7 by C5M. i used -ignh option also,still I am getting warning like H1 is

Re: [gmx-users] Implicit solvent & PBC

Simulation of a crystal in implicit solvent? Tsjerk On Fri, Sep 19, 2008 at 2:52 PM, Xavier Periole <[EMAIL PROTECTED]> wrote: > On Fri, 19 Sep 2008 17:28:20 +0530 (IST) > Anirban Ghosh <[EMAIL PROTECTED]> wrote: >> >> Hi All, >> >> I am simulating a Coarse Grained model using implicit solvent c

RE: [gmx-users] Implicit solvent & PBC

Hi, The same as in normal simulations. I always use PME and PBC in my implicit solvent simulations. Berk > From: [EMAIL PROTECTED] > Subject: Re: [gmx-users] Implicit solvent & PBC > To: gmx-users@gromacs.org > Date: Fri, 19 Sep 2008 14:52:39 +0200 > > On Fri, 19 Sep 2008 17:28:20 +0530 (IST)

[gmx-users] Re: reg: vectors

Hi, But if I want to look at the correlation function for an internal motion of a vector defined between two atoms, in that case whether the vectors are normalized or not are matter I suppose. Also, is it possible to monitor the dipolar correlation between two atoms of a protein ? Its always comp

Re: [gmx-users] Implicit solvent & PBC

On Fri, 19 Sep 2008 17:28:20 +0530 (IST) Anirban Ghosh <[EMAIL PROTECTED]> wrote: Hi All, I am simulating a Coarse Grained model using implicit solvent condition. Can Periodic Boundary Condition and Particle-Mesh-Ewald be used with implicit solvent simulation? What would be the use of PME a

[gmx-users] Implicit solvent & PBC

Hi All, I am simulating a Coarse Grained model using implicit solvent condition. Can Periodic Boundary Condition and Particle-Mesh-Ewald be used with implicit solvent simulation? Thanks, Anirban Ghosh M.Tech Bioinformatics University of Hyderabad Unlimited freedom, unlimited sto

Re: [gmx-users] dna-protein complex simulation

Hi Prasun, I converted it using a script of mine (which unfortunately is not in a shape for shipping yet), and the output file gives me no problem. Looking at it, I notice a difference (do look at it with a fixed-width font): dna.pdb:ATOM 7613 P DTHY I -72 17.935 138.346 27.497 1.00 81

[gmx-users] Re[2]: Segmentation fault in Gromacs 4.0 beta1

> Hi, > > I just noticed that for some time there has been a bug genbox in Gromacs 4 > that (always) caused a segv. > I have fixed it now. Berk, It's great! Thank you very much! -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email:

Re: [gmx-users] ask for help

zhang wrote: > > Dear all > Thank you for browsing my question.When I run a K ion channel, I added > DOPC bilayer membrane, at the first mdrun, Gromacs program got Range checking > error: > > Explanation: During neighborsearching, we assign each particle to a grid > based on its coordinat

Re: [gmx-users] Leaflet of Bilayer

minnale wrote: Hi Jochen thanks for your reply I have gone through this recent mail http://www.gromacs.org/pipermail/gmx-users/2008-September/036508.html more over if I use genconf command like this genconf -f .gro -o out -nbox 2 1 1 -dist 0 0 0 its adding 128 in eachleaflet I dont wany t

[gmx-users] dna-protein complex simulation

Hello Tsjerk I am attaching a file having a porttion of my PDB file,please check it.Its working for all other nucleotides.There is problem only with DTHY Thanx in advance with regards -- PRASUN (ASHOKA) dna.pdb Description: Protein Databank data ___

RE: [gmx-users] Re[2]: Segmentation fault in Gromacs 4.0 beta1

Hi, I just noticed that for some time there has been a bug genbox in Gromacs 4 that (always) caused a segv. I have fixed it now. Berk > Date: Wed, 17 Sep 2008 00:46:26 +0300 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gmx-users] Re[2]: Segmentation fault in Gromacs 4.0 beta

[gmx-users] RE: ask for help

> Explanation: During neighborsearching, we assign each particle to a grid > based on its coordinates. If your system contains collisions or parameter > errors that give particles very high velocities you might end up with some > coordinates being +-Infinity or NaN (not-a-number). Obviously, we can

Re: Re: [gmx-users] Leaflet of Bilayer

Hi Jochen thanks for your reply I have gone through this recent mail http://www.gromacs.org/pipermail/gmx-users/2008-September/036508.html more over if I use genconf command like this genconf -f .gro -o out -nbox 2 1 1 -dist 0 0 0 its adding 128 in eachleaflet I dont wany that many popc mole

[gmx-users] ask for help

Dear all Thank you for browsing my question.When I run a K ion channel, I added DOPC bilayer membrane, at the first mdrun, Gromacs program got Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains co

[gmx-users] RE: reg: vectors

> If not how can we obtain the correlation > function with normalized vectors using gromacs tools ? g_rotacf gives the ACF of the angle between two vectors. It is no difference if your vectors are unit-vectors or not. -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svobo

Re: [gmx-users] rmsip

Hi Sanjay, The matrix correlation coefficient (aka subspace overlap) calculated by g_anaeig is different from the RMSIP as calculated by the script. Cheers, Tsjerk On 9/19/08, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: > thanks Tsjerk for your help. > I have calculated RMSIP value and overla

[gmx-users] rmsip

thanks Tsjerk for your help. I have calculated RMSIP value and overlap matrix using g_anaeig with tag -inrp and -over. i wat to conferm that is it same a we got from script that sended by u??? can i beleive on this result or nedd to check by using script. thanks a lot sanjay _

Re: [gmx-users] dna-protein complex simulation

Hi Prasun, You probably weren't careful enough when changing the residue names. It seems the residue names need to be shifted by one position, and pdb2gmx reads DTHY as TH somehow, matching it to THF based on the first letters. The proper sed command for the conversion is: sed -e '{s/\(^.\{17\}\

Re: [gmx-users] Leaflet of Bilayer

minnale wrote: > > Hi all, >I have extended popc bilayer(intial popc.pdb from Dr.Tielmen site) by > using genbox command, I issued > genbox -cs popc128a.gro -o out.gro -box 9.2 9.2 6.9 it ran successfully with > increase of popc and water molecules. > Now I want to visualise this out fi

Re: [gmx-users] Re:GROMACS sample procedure

Hi, The gromacs wiki (wiki.gromacs.org) also lists a number of tutorials, written from different perspectives. But it doesn't have this one yet :p http://nmr.chem.uu.nl/~tsjerk/course/md-tutorial/ Any feedback is appreciated :) Cheers, Tsjerk On 18 Sep 2008 10:13:29 -, minnale <[EMAIL PRO

[gmx-users] Leaflet of Bilayer

Hi all, I have extended popc bilayer(intial popc.pdb from Dr.Tielmen site) by using genbox command, I issued genbox -cs popc128a.gro -o out.gro -box 9.2 9.2 6.9 it ran successfully with increase of popc and water molecules. Now I want to visualise this out file in VMD in a way that in ea