Re: [gmx-users] energy minimization - infinite force on atom

On 8/04/2010 4:23 PM, Evelyne Deplazes wrote: Hi gmx-users I am somehow famliar with gromacs but only used it with coarse grained force fields (Martini) so far, not with all atom ones. I am now trying to run a simulation on a membrane protein system (protein embedded in a POPC bilayer solvated w

[gmx-users] energy minimization - infinite force on atom

Hi gmx-users I am somehow famliar with gromacs but only used it with coarse grained force fields (Martini) so far, not with all atom ones. I am now trying to run a simulation on a membrane protein system (protein embedded in a POPC bilayer solvated with water) using the gromos force field (Gromacs

Re: [gmx-users] position_restraint anfd full Dynamics and berendsen Nose hoover Thermostat

On 8/04/2010 3:57 PM, shahid nayeem wrote: Please see the following pr.mdp and full.mdp pr.mdp You're using plain cut-off electrostatics, which was last acceptable in about 1958. :-) Get your system simulating stably at room temperature using a sensible electrostatics model before worrying

[gmx-users] Re:Re: g_nmeig_d error:cannot allocate region

Hi, I had checked and found that gromacs has been compiled in 64 bit mode. However still I am getting this error with "g_nmeig_d " command which says g_nmeig_d(1892) malloc: *** mmap(size=18446744072353271808) failed (error code=12) *** error: can't allocate region I am running this on a 8 no

Re: [gmx-users] position_restraint anfd full Dynamics and berendsen Nose hoover Thermostat

Please see the following pr.mdp and full.mdp pr.mdp cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 5 ; total 100 ps. nstcomm = 1 nstxout = 500 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = gri

Re: [gmx-users] Simulating a metal slab

On 8/04/2010 3:47 PM, radhika jaswal wrote: Hii Everybody... I want to simulate a Titanium Oxide slab of approx. 8-9 molecules in length and 4-5 molecules wide just as to mimic a rigid metal slab for further interaction studies. Can gromacs library support this and how I can do that... Yes, in

[gmx-users] Simulating a metal slab

Hii Everybody... I want to simulate a Titanium Oxide slab of approx. 8-9 molecules in length and 4-5 molecules wide just as to mimic a rigid metal slab for further interaction studies. Can gromacs library support this and how I can do that... All suggestions are welcome. Thanks Radhika

RE: [gmx-users] energy minimization in charged systems

What are the atoms that are causing the problems actually doing, where are they located etc? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +

[gmx-users] energy minimization in charged systems

Hi all, I am trying to simulate a electroosmotic flow in a nanochannel. System consists of water + (Cl-) ions in a channel confined of silicon <111> walls. I start with taking water as only solvent, equilibrating the system for about 12-15 ps (gmxcheck runs clean), and then use genion to insert (C

Re: [gmx-users] Fwd: help

On 8/04/2010 2:22 PM, Sepideh Soltani wrote: Please send one email, not three. If you learn how to use your tools properly, you make a much better impression of being someone worth someone else's time to help. -- Forwarded message -- From: *Sepideh Soltani* mailto:sepideh.sol

Re: [gmx-users] Memory corruption on SAS computation of a large (~1000000 frames) file

Thanks, I found the problem, I was using a wrong index file :P My bad, On Wed, Apr 7, 2010 at 8:32 PM, Mark Abraham wrote: > On 8/04/2010 10:22 AM, Camilo Andrés Jimenez Cruz wrote: > >> Hi all >> >> I am using gromacs-3.3.99's g_sas_s in a long trajectory and I get this >> error right away. I

[gmx-users] Fwd: moleculetype CU1+ is redefined

-- Forwarded message -- From: Sepideh Soltani Date: Thu, Apr 8, 2010 at 12:33 AM Subject: Fwd: moleculetype CU1+ is redefined To: sepideh.solt...@gmail.com Begin forwarded message: *From: *Sepideh Soltani *Date: *April 8, 2010 12:33:00 AM EDT *To: *gmx-us...@gromacs.org *Subj

[gmx-users] Fwd: help

-- Forwarded message -- From: Sepideh Soltani Date: Wed, Apr 7, 2010 at 11:21 PM Subject: help To: gmx-users-requ...@gromacs.org Hi all, I am running with gromacs 4.0.5. I am trying to do gromacs tutorial for drug-enzyme complex. I did this tutorial step by step but when I used

[gmx-users] header intact

-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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.or

Re: [gmx-users] Memory corruption on SAS computation of a large (~1000000 frames) file

On 8/04/2010 10:22 AM, Camilo Andrés Jimenez Cruz wrote: Hi all I am using gromacs-3.3.99's g_sas_s in a long trajectory and I get this error right away. I assume its memory capacity, is there a way (other than cutting the trj in smaller chunks?) Use a bigger computer? See g_sas -h for some b

[gmx-users] Memory corruption on SAS computation of a large (~1000000 frames) file

Hi all I am using gromacs-3.3.99's g_sas_s in a long trajectory and I get this error right away. I assume its memory capacity, is there a way (other than cutting the trj in smaller chunks?) Select a group: Select a group: *** glibc detected *** /usr/local/gromacs-3.3.99_20071008/bin/g_sas_s: mal

Re: [gmx-users] Potential Tables for user defined potentials

Justin A. Lemkul wrote: Gareth Tribello wrote: Hello again OK I have posted my notes on user defined potnetials here. I think there pretty exaustive (well they have everything I know about this in) and could be used as a how to in this form. However, I can't work out how to post them o

RE: [gmx-users] Lateral pressure profile in membrane simulations

Isn't that already present in the energy file, .edr, from the run? Simply use g_energy to extract it. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.mona

[gmx-users] Lateral pressure profile in membrane simulations

Dear users: I am doing some molecular dynamics simulations of membrane systems and i would like to ask you if someone know or have a code for the calculation of the lateral pressure profile from the data obtained doing membrane simulations. Thank you very much in advance, Fernando -- gmx-users

[gmx-users] Free Energy Calculations for linkage change in disaccharide

Dear All, In my previous email the text in the message was not shown. Thats why I'm writing this again. I request to see the attachment of earlier message. I'm sorry for this!! I have an disaccharide bound to a C-type lectin. The sequence of disaccharide is beta-galactose1-4beta-GlcNAc. The 3

[gmx-users] Re: converting parmbsc0 dihedrals to RB function

>From ffamber (in e.g. .../gromacs/top/ffamber99sbbon.itp): - impropers treated as propers in GROMACS to use correct AMBER analytical function - propers treated as RBs in GROMACS to use combine multiple AMBER torsions per quartet I followed these instructions while building acpypi (acpypi.googlec

Re: [gmx-users] problem with total energy

jampani srinivas ha scritto: > Dear Berk, > > I am sorry if i am confusing you with my poor description of problem, > actually I have submitted simulation with two temperature coupling groups (i > think you already know that from our earlier conversations) and found that > there is a continuous in

Re: [gmx-users] an energy minimization question, working with H-BONDS

Miguel Quiliano Meza wrote: Dear Users. I am a relative new user of GROMACS and I have some doubts: I would like to perform a energy minimization (with water and iones) of a crystal in orden to re-build the H-bonds responsible of the secundary structure, to achieve this goal I want to res

[gmx-users] an energy minimization question, working with H-BONDS

Dear Users. I am a relative new user of GROMACS and I have some doubts: I would like to perform a energy minimization (with water and iones) of a crystal in orden to re-build the H-bonds responsible of the secundary structure, to achieve this goal I want to restraint the movement of the protein (

[gmx-users] Free Energy Calculations for linkage change

Dear All, I have an disaccharide bound to a C-type lectin. The sequence of disaccharide is beta-galactose1-4beta-GlcNAc. The 3'OH and 4'OH of beta-galactose coordinate to the Ca2+ at the active site. FRET experiments have shown that if the disaccharide linkage is changed to beta-galactose1-3bet

Re: [gmx-users] position_restraint anfd full Dynamics and berendsen Nose hoover Thermostat

On 7/04/2010 9:08 PM, shahid nayeem wrote: Dear users Please let me know some basic question. I am sorry if I am asking a silly question. a) While simulating a protein thermal unfolding at high temperature say 500K should I run position restraint dynamics at 500k or at 298K. I am doing 100ps posi

Re: [gmx-users] coarse-grained model of POPC in Martini coarse-grained force field?

POPC lipid is defined in the lipid itp file you'll find on the website. http://md.chem.rug.nl/cgmartini/index.php/forcefield-parameters/56-lipids POPC coordinate file is indeed not present on the website. However, transforming a DOPC or DPPC coordinate file to a POPC coordinate file goes only b

Re: [gmx-users] converting parmbsc0 dihedrals to RB function

On 7/04/2010 7:44 PM, Vigneshwar Ramakrishnan wrote: Dear Users, I am trying to port the new parmbsc0 forcefield (http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0) into gromacs for DNA simulations. While unit conversions are sufficient to convert many of the parameters from AMBER to GROMACS format

[gmx-users] coarse-grained model of POPC in Martini coarse-grained force field?

I'd like to run simulations with coarse grained model lipid bilayer.  I can not  find the force field for coarse grain POPC lipid or equilibrated bilayer coordinates in Martini website. Please help me! thank you! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs

[gmx-users] position_restraint anfd full Dynamics and berendsen Nose hoover Thermostat

Dear users Please let me know some basic question. I am sorry if I am asking a silly question. a) While simulating a protein thermal unfolding at high temperature say 500K should I run position restraint dynamics at 500k or at 298K. I am doing 100ps position restraint dynamics at 500k. Am I right i

[gmx-users] Re: Query regarding Gromacs

Please keep all Gromacs-related correspondence on the gmx-users list. I am not a private tutor or help service, and you stand a much better chance of getting an answer by contacting the community. I have never worked with a system like yours, so I don't know why you'd assume I have such a p

Re: [gmx-users] Regarding inflategro.pl

Jignesh Patel wrote: Dear Justin, When I used inflategro.pl , it removed original water molecules of DPPC128 membrane. After that i added water using genbox. Is it correct method to follow? Yes. -Justin Thanking you in anticipation. -- Best Wishes, Jignesh Pate

[gmx-users] Regarding inflategro.pl

Dear Justin, When I used inflategro.pl, it removed original water molecules of DPPC128 membrane. After that i added water using genbox. Is it correct method to follow? Thanking you in anticipation. -- Best Wishes, Jignesh Patel Pharmacoinformatics, NIPER -- gmx-users mailing listgmx-user

[gmx-users] Re: loab imbalance

> The first time I did not notice that 16 cpus are twice as slow as 8. > Are you really sure you did not mix things up? > The other way around the timings would make perfect sense. > If not, there is a problem with your 16 cpu simulation. > > What load imbalance is reported for the 8 cpu run? > >

[gmx-users] Re: converting parmbsc0 dihedrals to RB function

I strongly advice you to contact Eric Sorin from ffAMBER project as he's onto that and you maybe can add to his efforts. http://ffamber.cnsm.csulb.edu/ Alan On Wed, Apr 7, 2010 at 11:00, wrote: > I am trying to port the new parmbsc0 forcefield ( > http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0

[gmx-users] converting parmbsc0 dihedrals to RB function

Dear Users, I am trying to port the new parmbsc0 forcefield ( http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0) into gromacs for DNA simulations. While unit conversions are sufficient to convert many of the parameters from AMBER to GROMACS format, dihedral angle conversion does not seem to be stra

RE: [gmx-users] Re: loab imbalance

> From: zhao0...@ntu.edu.sg > To: gmx-users@gromacs.org > Date: Tue, 6 Apr 2010 20:45:37 +0800 > Subject: [gmx-users] Re: loab imbalance > > > > > > On 6/04/2010 5:39 PM, lina wrote: > > > > > Hi everyone, > > > > > > > > > > Here is the result of the mdrun which was performed on 16cpus. I am

RE: [gmx-users] link gromacs i7

Hi, I am using openmpi 1.2.8 and it works fine. You get 15% performance increase when going from 4 to 8 processes. Note that with 4 processes you have to use: mpirun -np 4 taskset 0xf mdrun ... to avoid two processes running on the same physical core. The only problem I can think of is that your

Re: [gmx-users] link gromacs i7

We have been using gromacs-4.0.7 on I7 with up to 8 CPUs. The scaling is pretty good. Note that upgrading to openmpi-1.4.1 was necessary to be able to scale to up to 8 CPUs, if not the jobs where hanging ... Since you have it already, I do not see where the problem can come from. Are you sure you

Re: [gmx-users] Protein is having non-integral charge

On 7/04/2010 4:03 PM, sonali dhindwal wrote: Hello All I am using gromacs for simulating my protein I got after homology modelling. While doing this when I get toplogy file by using 0: GROMOS96 43a1 force field topology file I am getting has most of the residues having non-integral charge. Can so