Re: [gmx-users] how to switch from NPT to NVT ensemble during equilibration

On 10/02/2011 10:54 AM, Rini Gupta wrote: Dear gmx users, I am using gromacs (version 4.0.7) first time to setup a 2-butoxyethanol-water simulation. I created topology and coordinate file for BE using AUTOMATED TOPOLOGY BUILDER server. It created a topology file (for united atom) compatible wit

Re: [gmx-users] Domain decomposition configuration

On 10/02/2011 8:10 AM, Justin A. Lemkul wrote: Denny Frost wrote: Is tpbconv with the "pbc" option the best way to make the molecules whole again? The only way, as far as I'm aware (aside from editconf's crude approach). Do this before you concatenate your systems. And you will then ha

Re: [gmx-users] localpressure.dat file not created

On 10/02/2011 11:48 AM, ma...@physics.ucsb.edu wrote: I successfully ran version 4.5.3 to simulate a small DPPC bilayer patch using the files from Marrink's website by typing: /usr/bin/grompp -v -f mem.mdp -c mem.gro -p mem.top -o topol.tpr -maxwarn 100 mdrun In the .mdp file I then added the

Re: [gmx-users] Domain decomposition configuration

On 10/02/2011 12:45 PM, Justin A. Lemkul wrote: Mark Abraham wrote: On 10/02/2011 8:10 AM, Justin A. Lemkul wrote: Denny Frost wrote: Is tpbconv with the "pbc" option the best way to make the molecules whole again? The only way, as far as I'm aware (aside from e

Re: [gmx-users] More than one settle type.

On 11/02/2011 2:50 PM, Sikandar Mashayak wrote: Hi I am performing SPC/E water simulation where I want to fix location of one water molecule and let others move. To do that I have defined two groups with name SOL0 and SOL, where SOL0 has just one water molecule and SOL grp contains all others

Re: [gmx-users] crashed simulation: simulation of docked proteins in spc water crashes with LINCS warning

On 11/02/2011 3:47 PM, Sanjay Kumar Upadhyay wrote: Dear gmx-users I am experiencing some problems running a protein-protein docked structures in water(GROMOS43a1/SPC)with gmx-4.0.4 using 8 CPUs. I have 20 docked (protein-protein) structures of one common protein with two different homologous p

Re: [gmx-users] Re: Extending the simulation

On 11/02/2011 8:10 PM, bharat gupta wrote: Hi, I extended by 3ns simulation by 2 more ns ... i.e total 5 ns but the .xtc file shows only the 3ns trajectories and after checking the md.log file , its showing that it completed those 2 ns steps also... then how can I get the trajectory for those

Re: [gmx-users] PRODRG

On 11/02/2011 8:18 PM, mohsen ramezanpour wrote: Dear Dr.Justin I did it,it works.Thanks. there are another problem: I want to add some hydogens to my topology. I used ADDHYD atomname,But this dosen't work. PLease let me know how can I include some Hydrogenes in my topology. As Justin suggest

Re: [gmx-users] Re: crashed simulation: simulation of docked proteins in spc water crashes with LINCS warning (Mark Abraham)

On 11/02/2011 9:14 PM, Sanjay Kumar Upadhyay wrote: Sorry, in previous mail i did not write md protocol in details what i followed for simulation. after energy minimization steps i did PR for 200 ps and then run the production MD. Even i did vacuum energy minimization before adding solvent for al

Re: [gmx-users] NVT run

On 12/02/2011 12:02 AM, Thomas Koller wrote: Hello, I calculate the density of my lquid in the equilibrated time range of the density-time plots (NPT runs). I use the gro file of these NPT runs for NVT runs to calculate the self diffusion coefficient at the simulated density. Concerning this

Re: [gmx-users] Performance in ia64 and x86_64

On 11/02/2011 11:33 PM, Ignacio Fernández Galván wrote: Hi all, I'm compiling and testing gromacs 4.5.3 in different machines, and I'm wondering if it's normal that the ia64 is much slower than the x86_64 I don't know full details of the machines, because I'm not the administrator or owner, bu

Re: [gmx-users] Fwd: Question on Gromacs: rlist, rvdw, rcoulomb

I am a user of gromacs. I am quite confused when I came across the relation of rlist and rvdw / rcoulomb in vdw and coulomb calculation. In cut-off, it says rvdw / rcoulomb should be greater than rlist, while in switch/shift, it says rvdw should be smaller than rlist... I guess in cut-off, it's

Re: [gmx-users] doubts on g_confrms output

On 12/02/2011 2:55 AM, Kwee Hong wrote: Hi Tsjerk, Thanks for the help. I got it. But do you have any idea how to solve this in vmd? Use trjconv -sep on the .pdb file to split it. Mark Regards, Joyce *From:* Tsjerk W

Re: [gmx-users] extracting a structure from confout.gro file

On 12/02/2011 1:51 AM, Justin A. Lemkul wrote: najwa drici wrote: hi all I would like to extract my protein structure with the first hydration shell around the active site which contains an ion from counfout.gro. Is there any program script able to do this? Not in one step, no. You cou

Re: [gmx-users] Performance in ia64 and x86_64

On 12/02/2011 12:44 AM, Ignacio Fernández Galván wrote: Original Message From: Mark Abraham We can't say with the information given. For best performance, the number of threads cannot exceed the number of physical cores available to one processor. To go higher, you need to co

Re: [gmx-users] Add custom residue to DNA index group

On 12/02/2011 3:14 AM, william Stebbeds wrote: Hi Folks, I have added a custom DNA residue to the amber99sb ff, and everything works perfectly, (thanks to Justin!). The residue is incorporated perfectly into the sequence, with no abnormal events during simulations. I have updated all the fil

Re: [gmx-users] doubts on g_confrms output

hand in a text editor. Mark *From:* Mark Abraham *To:* Discussion list for GROMACS users *Sent:* Saturday, February 12, 2011 0:01:39 *Subject:* Re: [gmx-users] doubts on g_confrms output On 12/02/2011 2:55 AM, Kwee

Re: [gmx-users] Terminus Atoms genrestr?

On 12/02/2011 7:18 AM, Teemu Murtola wrote: Still, the only critique I've heard so far (from several people, it seems) is a vague "the documentation sucks", which doesn't really help in improving things, or even figuring out where people face problems. g_select does provide some on-line help (by

Re: [gmx-users] genbox error

On 12/02/2011 7:51 AM, Rini Gupta wrote: Dear gmx users, I am using gromacs (version 4.0.7) to setup a 2-butoxyethanol-water simulation. I created topology and coordinate file (.pdb) for BE using AUTOMATED TOPOLOGY BUILDER server. It created a topology file (for united atom) compatible with GRO

Re: [gmx-users] genbox error

On 12/02/2011 12:22 PM, Justin A. Lemkul wrote: Do the -ci and -cs steps separately and see if that gives you the proper output. I have found that the two are incompatible, but in theory, I don't know why one couldn't do everything in one step. It can depend on the assumptions about the purp

Re: [gmx-users] genbox error

On 12/02/2011 12:51 PM, Rini Gupta wrote: Hello Mark, Thanks for the reply. I tried to first make a box using editconf editconf_d_mpi -f conf.gro -o be.gro -bt cubic -box 2.7 2.7 2.7 Box is successfully created and then I use genbox_d_mpi -cp be.gro -p topol.top -ci be.gro -nmol 19 -o out.gr

Re: [gmx-users] doubts on g_confrms output

uld be, however. Mark Cheers, Tsjerk On Feb 12, 2011 2:19 AM, "Mark Abraham" <mailto:mark.abra...@anu.edu.au>> wrote: On 12/02/2011 3:45 AM, Kwee Hong wrote: > > Hi Mark, > > I tried but with this error: > > Fatal erro... OK. I don't know why two f

Re: [gmx-users] how to fixe distance

On 13/02/2011 9:03 AM, najwa drici wrote: hi all How can I fix some distances and angles in manner, that I can set up long molecular dynamic simulation without structural lost? Look up "restraints" in the manual. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs

Re: [gmx-users] FEP energy errors with positional restraints?

On 13/02/2011 11:49 AM, TJ Mustard wrote: Hi all, I have been testing the ability of taking a sphere of a protein around a ligand, and positionally restrain the specified alpha carbons. I was hoping to keep non connected protein chains from drifting apart. I have been able to run these md/fe

Re: [gmx-users] FEP energy errors with positional restraints?

On 13/02/2011 3:57 PM, TJ Mustard wrote: On February 12, 2011 at 5:35 PM Mark Abraham wrote: On 13/02/2011 11:49 AM, TJ Mustard wrote: Hi all, I have been testing the ability of taking a sphere of a protein around a ligand, and positionally restrain the specified alpha carbons. I was

Re: [gmx-users] FEP energy errors with positional restraints?

On 13/02/2011 5:03 PM, TJ Mustard wrote: On February 12, 2011 at 9:31 PM Mark Abraham wrote: On 13/02/2011 3:57 PM, TJ Mustard wrote: On February 12, 2011 at 5:35 PM Mark Abraham <mailto:mark.abra...@anu.edu.au> wrote: On 13/02/2011 11:49 AM, TJ Mustard wrote: Hi all,

Re: [gmx-users] FEP energy errors with positional restraints?

On 13/02/2011 6:07 PM, TJ Mustard wrote: On February 12, 2011 at 10:14 PM Mark Abraham wrote: On 13/02/2011 5:03 PM, TJ Mustard wrote: On February 12, 2011 at 9:31 PM Mark Abraham <mailto:mark.abra...@anu.edu.au> wrote: On 13/02/2011 3:57 PM, TJ Mustard wrote: On Febru

Re: [gmx-users] Gromacs Installation

On 15/02/2011 4:35 PM, majid hasan wrote: Okay, I'll do this. I have also realized after browsing through config.log, that Xlib.h is absent. Where do I get it, I want it to run ngmx. You will need the X windowing system installed, and probably the associated "devel" packages. Use your distrib

Re: [gmx-users] on force fields

On 16/02/2011 3:41 PM, Mr Bernard Ramos wrote: Hi everyone! I need to update the gromos force field 53A6 with the new force field 53ACARBO (JCC 10 NOV 2010). 1. I will have to change the parameter values in the file ff_bonded.itp and ff_nonbonded.itp in the gromos53a6.ff. Are these the only fi

Re: [gmx-users] g_rmsf reference structure?

On 16/02/2011 3:44 PM, kulleperuma.kulleper...@utoronto.ca wrote: Dear all, I use g_rmsf of Gromacs VERSION 4.0.5 to calculate the RMSF of the C-atoms with reference to the average structure between 5-10 ns of a total of 10 ns simulation as below; g_rmsf ?f md.xtc ?s md.tpr ?b 5000 ?e 1

Re: [gmx-users] Conatant pH simulation in GROMACS

On 16/02/2011 6:04 PM, bipin singh wrote: Hi all, I want to know that, whether we I can do constant pH simulation in gromacs. Please provide some details regarding this. Please search first ;-) http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation Mark -- gmx-users mailing li

Re: [gmx-users] Re: Periodic Boundary Conditions g_mindist -pi

On 16/02/2011 10:30 PM, ifat shub wrote: Hi Tsjerk, Thank you for your reply. I am aware of the trajconv option but I wanted to know if there is a way to avoid these kind of jumps over the periodic boundaries during the mdrun and not post process? No. mdrun does not know in advance what your

Re: [gmx-users] initial structures for md simulations

On 16/02/2011 11:24 PM, oguz gurbulak wrote: /Dear All/, I want to generate some initial crystalline structures of my targetmolecules for md simulations. /Are there any free softwares/ to do this? Some sources for obtaining initial coordinates can be found here http://www.gromacs.org/Doc

Re: [gmx-users] mismatch between energies of sequential minimization runs

On 17/02/2011 6:47 PM, Efrat Noy wrote: Hi, I am running 2 sequential minimizations with the same mdp file. As expected the second minimization stops in step zero and the resulting structures of the 2 minimization runs are identical (RMSD=0.0). But, the energies of the last step of the first m

Re: [gmx-users] backbone_few_sidechain_fixed

On 18/02/2011 5:14 PM, shahid nayeem wrote: Dear All My protein complex has three chains A B C. I created three posre.itp for backbone and some side chain which is not on the interface for each of the chain. I put these in .top file as follows ; File 'complex.top' was generated ; By

Re: [gmx-users] saving velocities and coordinates frequently

On 18/02/2011 12:21 PM, Amit Choubey wrote: Hi , I wish to save velocities and coordinates every step for my system. For saving disk space i dont want to save water molecules. How can i do this ? See www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume Mark -- gmx-users

Re: [gmx-users] about -CN triple bond

On 18/02/2011 1:13 PM, C.Y. Chang wrote: Hi, I am dealing with the lipid bilayer permeation simulation. Most compounds can be finished, but the compounds with CN can't be performed simulation. I have searched the discussion in the gmx-users discussion. The "vsite" has been mentioned, and I hav

Re: [gmx-users] configure: error: cannot compute sizeof (off_t)

On 19/02/2011 2:32 PM, Justin Kat wrote: Dear experts, I have installed Gromacs under the normal configuration and am now attempting to install the mpi version of mdrun on a machine, however I am getting this error during the configuration: configure: error: cannot compute sizeof (off_t) See

Re: [gmx-users] about -CN triple bond

type 1000 GROMACS didn't recognise the mis-spelled directive, and so it's trying to make sense of your position restraint lines as dihedrals. Mark Chia-yun 2011/2/18 Mark Abraham <mailto:mark.abra...@anu.edu.au>> On 18/0

Re: [gmx-users] about -CN triple bond

16 and equation 4.134. Mark Thanks for your help. Best, Chia-yun 2011/2/19 Mark Abraham <mailto:mark.abra...@anu.edu.au>> On 19/02/2011 3:02 PM, C.Y. Chang wrote: Hi, I have tried to add [ position restraints ] This is misspelled. Surel

Re: [gmx-users] configure: error: cannot compute sizeof (off_t)

On 23/02/2011 3:35 PM, Justin Kat wrote: Im not quite sure if this is the right place to analyze, but a bit before the part in the config.log where it states the error of "cannot compuete sizeof (off_t)", there is this: configure:25048: checking size of off_t configure:25053: /usr/local/bin/

Re: [gmx-users] scaling of replica exchange

On 02/23/11, Valeria Losasso wrote: > > Dear all, > I am making some tests to start using replica exchange molecular dynamics on > my system in water. The setup is ok (i.e. one replica alone runs correctly), > but I am not able to parallelize the REMD. Details follow: > > - the test is on 8

Re: [gmx-users] scaling of replica exchange

h others' toes. Mark > Valeria > > > > On Wed, 23 Feb 2011, Mark Abraham wrote: > > > > > > >On 02/23/11, Valeria Losasso wrote: > > > >  Dear all, > >  I am making some tests to start using replica exchange molecular > >dynamics

Re: [gmx-users] scaling of replica exchange

er case and not more. > That's going to affect the usefulness of doing replica-exchange, but not the computational performance when doing it. Doing exchanges that never/always succeed makes essentially no difference to the performance. Mark > On 02/23/2011 10:31 AM, Mark Abraham w

Re: [gmx-users] trr files transferability

On 24/02/2011 9:44 AM, Ravi Bhadauria wrote: Hi all, I have a simple question about trr files. Are they transferable across different version(s), and more importantly, different bit architectures (32bit to 64bit and vice versa). Please let me know. All GROMACS file formats are insensitive to

Re: [gmx-users] Performance in ia64 and x86_64

On 25/02/2011 8:25 PM, Ignacio Fernández Galván wrote: I wrote: It seems the x86_64 processor has 4 cores and 8 threads support (), so the machine has probably two physical processors. I thought MPI was only needed if there was network communication

Re: [gmx-users] index file groups

On 25/02/2011 6:37 PM, Nick wrote: Hello to all, Please help me with the following questions. Your attention is greatly appreciated. 1- I have an inquiry about index groups. If I specify all my solute chains as a whole in one group [all chains] (including n chains having m atoms each) and c

Re: [gmx-users] AlF4 - producing LINCS errors

On 02/28/11, Matthew Cliff wrote: > Hi, > >     I'm very new to MD and I am trying to run MD simulations of proteins > binding AlF4-. I am running GROMACS 4.5.3 > and using OPLSAA forcefield, Tip4p water. > I have created a topology file for AlF4 (see below), and added atom types to > the fo

Re: [gmx-users] about -CN triple bond

ntral C atom as a dummy. That reduces your number of non-virtual co-linear atoms to 2 in all cases. That solves this problem. Mark > > Thaks a lot. > Best, > >        Chia-yun Chang > > > > > 2011/2/19 Mark Abra

Re: [gmx-users] about -CN triple bond

Chia-yun Chang 2011/2/28 Mark Abraham <mailto:mark.abra...@anu.edu.au>> On 02/28/11, *"C.Y. Chang" * mailto:chiayun.ch...@gmail.com>> wrote: Hi, I try to add a dummy atom in my small molecular pdb and topology file. (attached files) But

Re: [gmx-users] isopeptide bond

On 03/01/11, zeppelin zeppelin wrote: > > Dear GROMACS users, > > > > I started to work with gromacs (version > 4.0.5) only several weeks ago and I need your help. > > > In that case, you'll be best served by starting with the most recent version of GROMACS, not one that's 3 years old.

Re: [gmx-users] Re: Nitrogen box

On 03/01/11, sarah k wrote: > Dear Justin, > Thanks for your reply. Now, I have problem in generationg the > coordination file. Since my molecule is diatomic, the PRODRG server > fails and when I used another parametrization tool, the output files > were void. Can I generate the file in gromacs

Re: [gmx-users] .tdr file not created

On 03/01/11, sakthi kumaran wrote: > > > Dear Sir, > >    I copied the tutor folder to some local path(say Dektop) and tried to > execute from there. So the problem of secyurity issues with acces previleges > won,t be there I think. BUt still I am not able to run the examples.Whether

Re: [gmx-users] .tdr file not created

On 03/01/11, sakthi kumaran wrote: > Sorry for making my statement unclear. > >   > > I copied the tutor folder to desktop and tried to run it from there. But when > I entered the grompp -v command as mentioned in the manual, the .tdr file is > not getting created. So without the .tdr file

Re: [gmx-users] index file groups

On 26/02/2011 3:09 AM, Moeed wrote: Thank you Mark for your detailed explanation. Sorry if I am slow in understanding some stuff. I appreciate your patience. 1- I have an inquiry about index groups. If I specify all my solute chains as a whole in one group [all

Re: [gmx-users] mpi run in Gromacs

On 2/03/2011 11:37 PM, Erik Marklund wrote: Selina Nawaz skrev 2011-03-02 11.54: Hi, I am a Phd student studying polymer membranes. I have installed Gromacs version 4.5.2 on our department cluster and attempted to run a simulations on a DPPC bilayer membranes taken from the tielleman website.

Re: [gmx-users] Re: adding ff parameter of modified residue to charmm ff

On 03/03/11, bharat gupta wrote: > Hi, > > I followed the tutorial > - http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field for > updating the Charmm FF for my modified residue .. > > > > I added the residues to the .rtp file , then I added the new atom types in

Re: [gmx-users] REMD simulation of peptide-membrane system

On 03/03/11, Jianguo Li wrote: > > > > > > Dear all, > > I'd like to do folding simulations of a short peptide on membrane surface > using REMD using atomistic FF. But the problem is that membrane will disrupt > at high temperatures. To maintain the membrane structure, I am thinking the

Re: [gmx-users] How to find average protein structure.

On 4/03/2011 4:40 PM, ajanihar...@gmail.com wrote: Hi everybody, I am new user of gromacs. I had run simulation for 1ns and have obtained all required output files. After comparing and analysing the potential energy and rms . Now i want to know how to find out the average protein structure be

Re: [gmx-users] different RMSD graphs after using pbc mol

On 4/03/2011 4:53 PM, גדעון לפידות wrote: Hi all, I was wandering if anyone knows of a problem with gromacs 4.0.7 when it comes to its RMSD tool. After running a 44 ns simulations on a soluble protein I used g_rms to calculate RMSD . The results did not seem to make sense ( >30 angstrom at som

Re: [gmx-users] calcium diffuses away from the protein during MD

On 4/03/2011 4:55 PM, Sunita Patel wrote: Dear Users, I performed MD simulation on a calcium binding protein with bound calcium starting from the crystal structure using gromos96 forcefield with explicit solvent with NVT ensembles. I performed energy minimization of calcium bound protein with wa

Re: [gmx-users] trajectory output from g_select ?

On 4/03/2011 11:01 AM, jk...@ifr88.cnrs-mrs.fr wrote: Hi, I'm using g_select ( great tool !) to isolate a series of identical molecules, and I need to run some gmx analyses of heavy trajectories. If the number of molecules selected is constant over all the frames, it's possible to rebuild a

Re: [gmx-users] MD of a crystall structure

On 4/03/2011 12:41 AM, Hernan Ahumada wrote: Dear users I am trying to make MD of a crystal structure of carborane. This molecule is a ridge cage of 12-vertex (C2B10H12). I have all the bonding and non-bonding parameter from amber and I am working with this condition, for LJ interaction using s

Re: [gmx-users] Re: adding ff parameter of modified residue to charmm ff

1c CT2 HB 48.000 108. CP2C NR1C CT2 36.00129.00 CP1C NR1C CT2 32.00123.40 On Thu, Mar 3, 2011 at 1:23 AM, Mark Abraham <mailto:mark.abra...@anu.edu.au>> wrote: On 03/03/11, *bharat gupta * mailto:bharat.85.m...@gmail.com>> wrote: Hi, I followed

Re: [gmx-users] trajectory output from g_select ?

On 04/03/11, jonathan wrote: > Indeed, to be more specific, I would like to run a g_covar analysis on > lipid acyl chains that are within a certain distance to a protein. > Since the trajectories are quite long (+10K frames), splitting each > frame to separate files, and then isolating the sele

Re: [gmx-users] trajectory output from g_select ?

On 05/03/11, jonathan wrote: > I previously supposed that the number of lipids selected was constant to > simplify the problem. > > The distance criteria gives a different number of lipids for each frame. > To end up with  a constant number of atoms in the output trajectory, > each lipid select

Re: [gmx-users] number of DD cells

On 05/03/11, "Justin A. Lemkul" wrote: > > > Moeed wrote: > >Hello, > > > >I am attempting to increase the density using NPT. As I increase the > >pressure to compress the system after some steps simulation crashes. I > >thought maybe its becasue I am compressing too fast but even when I ta

Re: [gmx-users] Dihedral Restraints

On 05/03/11, Sai Pooja wrote: > Hi, > >   > > In Manual 4.5.3, the potential for dihedral restraints is the following: > >   > > Phi* = (Phi - Phi0)MOD 2Pi > >   > > Where Phi is the instantaneous dihedral and Phi0 is the reference dihedral. > And the MOD2Pi, I assume, ensures a differen

Re: [gmx-users] questions regarding cutoff, charge groups, thermocouple and equlibration

On 05/03/11, Kavyashree M wrote: > > > On Sat, Mar 5, 2011 at 12:22 AM, Justin A. Lemkul wrote: > > > > > > > > > > > > > > > > > It is difficult to say for certain how OPLS should be used with MD, since > > it was originally designed for different software doing MC simulations.  I

Re: [gmx-users] Warning: 1-4 interaction

On 06/03/11, Moeed wrote: > Hi everyone, > > My attempt to conduct a NPT failed although everything seemed to be going > well. Topology is OK and I am just curious why system is blowing up all of a > sudden towards the end of simulation. I should mention that by changing > fourierspacing fr

Re: [gmx-users] # Protein non-integer charge‏

On 8/03/2011 1:11 AM, Marcelo Silva wrote: Hi everybody, My problem is the following: I am studying the chromosome partitioning protein ParB from Burkholderia cenocepacia J2315. As no crystal structure was available, I used I-TASSER to predict its 3d structure. In order to refine the structu

Re: [gmx-users] RMSD truncation Restart simulation problems

On 7/03/2011 8:23 PM, Henri Mone wrote: Dear Gromacs Users/ Experts and Beginners, I'm using Gromacs 4.5.3 to run REMD simulation. The REMD simulations stooped abruptly and therefore the replicas have uneven information. One of the checkpoint differ in time and frame compared to other replicas.

Re: [gmx-users] g_RMS: Mismatch of atom number between topology and reference structure

On 7/03/2011 7:33 PM, Sergio Manzetti wrote: Hello, I am doing a refolding experiment, but I re-experience the same error. First of all, I use pdb2gmx for an input PDB structure, choose OPLS/AA force field and vacuum settings (no waters). Then I amke a box, and start simulations. What I want

Re: [gmx-users] Re-compile Gromacs Program?

On 08/03/11, Chih-Ying Lin wrote: >   > >   > > Hi > > I found the Gromacs Program could not do the parallel computing > since the staff of the compter center in my school upgraded the intel > compiler to v 12, and rebuilt the mpich build with intel. I requested them to > recompile the Gr

Re: [gmx-users] Disable non-bonded interactions between molecules

On 08/03/11, rue...@mpip-mainz.mpg.de wrote: > Dear all, > > I need to perform a simulation in which interactions between molecules > (polymers) are calculated only via virtual sites. Within a molecule, > non-bonded interactions between atoms should be present. Further, it would be > best to

Re: [gmx-users] QMMM

On 8/03/2011 4:48 PM, Haresh wrote: Hello everyone, I want install gromacs with mopac7 for qmmm. Can you guide me for installation procedure There's a guide on the GROMACS webpage. Please search the web before asking questions :) Mark -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Unsupported box diagonal

On 8/03/2011 3:58 PM, Sweta Iyer wrote: Hi, I am trying to do a simple membrane simulation of a h4 residue helix in DMPC. However, I encounter a strange issue this time when i try to run the final production run. the error that i get is as follows: Looks like you haven't equilibrated well enoug

Re: [gmx-users] using one thermostat for entire system ??

On 8/03/2011 2:50 AM, Jennifer Williams wrote: Hi, I simulated the diffusion of small gases (CO2, N2) in a framework structure which was mostly frozen with some mobile surface groups. I applied a temperature thermostat to the entire system (i.e I didn't couple the gas molecules and framework

Re: [gmx-users] Instantaneous Square Displacement

On 8/03/2011 3:01 AM, Jennifer Williams wrote: Hi, I am writing a paper where I describe that gas molecules move inside a pore and then stick for long periods of time in occlusions in the pore wall. A reviewer has mentioned that I could illustrate this effect by using "instantaneous square

Re: [gmx-users] g_energy inconsistent results

On 8/03/2011 9:44 PM, Ehud Schreiber wrote: Dear Gromacs users, I am working with version 4.5.3, using the opls-aa forcefield in an implicit solvent, all-vs-all setting: pdb2gmx -ter -ff oplsaa -water none -f file.pdb I am energy-minimizing structures in 3 stages (steep, cg and l-bfgs). Th

Re: [gmx-users] RMSD truncation Restart simulation problems

On 8/03/2011 9:41 PM, Henri Mone wrote: Hi All, hi Mark, Here are some more details. The outputs and error messages are attached at the end of the e-mail. After truncation I get the error message [1a], gromacs has problems with the checksum of the trr fles. After truncation the trajectories (xtc,

Re: [gmx-users] parallel running

On 9/03/2011 1:51 AM, mohsen ramezanpour wrote: Dear Dr.Justin Thank you for your notice. I don't know the problem is related to MY COMMAND or to CLUSTER CONFIGURATION. please look at my commands and let me know the answer of this question.just this. The command you posted said that your comp

Re: [gmx-users] g_rms and g_cluster

On 09/03/11, shahid nayeem wrote: > Hi Justin > If I make an index group with backbone and CA C N O group of the > concerned residues and then do least square fitting then do this > fitting is equivalent to backbone fitting first and then translating > to coincide CA of the residue of interest.

Re: [gmx-users] Density of water, Dispcorr and rmsd

On 9/03/2011 10:43 PM, Kavyashree M wrote: Dear users, What is the difference between densities predicted by tip4p and spc models? I am using tip4p (with OPLSAA forcefield) in the simulation, during position restrained dynamics, Average water density is around 1015kg-m-3 at 300K which is

Re: [gmx-users] Definition of helicity

On 10/03/2011 12:58 AM, cd...@ipc.uni-karlsruhe.de wrote: > Hi Justin, > > Thank you for your notice. > I am afraid my explanation was not enough. > When protein atoms is specified, g_helix seems to calculate the > helicities for all residue. > And then, the helicity value of each residues is writt

Re: [gmx-users] secondary structure propensities of residues

On 10/03/2011 1:36 AM, Justin A. Lemkul wrote: ZHAO Lina wrote: Hi, How do get the percentage of the secondary structure propensities of residues? seems dssp none such effect? The scout.xvg file contains everything you need (in a broad sense) - number of residues in a given secondary s

Re: [gmx-users] Zero Potential of Mean Force with g_wham

On 10/03/2011 1:43 AM, Susana Tomasio wrote: Thank you Jianguo. So can I use g_wham 4.5.2 even though I ran the simulations on 4.5.1? Quite likely. Check the change logs on the GROMCACS website for relevant issues. Mark Best regards, Susana On Wed, Mar 9, 2011 at 2:31 PM, Jianguo Li

Re: [gmx-users] Treatment of protein termini when there are missing residues

On 10/03/11, "Justin A. Lemkul" wrote: > > > jo hanna wrote: > >Hello, > > > >My question concerns the 'best' way to treat the terminal groups for a > >protein that is missing residues at both termini, e.g. a 530 residue protein > >where only residues 15-512 are present in the pdb. > > > >M

Re: [gmx-users] Regarding Gromacs Application in more than 10 node cluster

On 11/03/11, Kannan Govindarajan wrote: > Hi, > > I am trying to running the Gromacs application in more than 10 node beowulf > cluster if i run the gromacs application in 5 node cluster it is not > > showing any error. If i increase the number of nodes it throws the > communication error i

Re: [gmx-users] .cpt and .trr files

On 11/03/11, Anna Marabotti wrote: > > > > > > > > > > Dear > all, > > a very quick > question: I > would like to know if a checkpoint file produced with a simulation with > Gromacs > contains really ALL information needed to restart a simulation; or better, if > I > keep only th

Re: [gmx-users] terminated but not completely

On 13/03/2011 8:53 AM, mohsen ramezanpour wrote: Dear All I run a simulation for 4 days. Unfortunately it terminated,but not completely,1 steps from 2 has done. Is there any way to run the continue of my files? Thanks in advance for your guidances Best Regards http://www.gromacs.org

Re: [gmx-users] isopeptide bond

On 13/03/2011 8:55 PM, Yulian Gavrilov wrote: Dear gmx users, I just started with gromacs. Can you help me to find my mistake? I already asked about it, but I did not understand what to do exactly in my case. I try to run to add a new *isopeptide bone* to connect Lys and Gly (to make a tet

Re: [gmx-users] isopeptide bond

, and go and look at the topology to see what atoms have made a bond. Mark When I look on step...pdb, one these residues is exploded (it's atoms are far from each other outside of the water box). 2011/3/13 Mark Abraham <mailto:mark.abra...@anu.edu.au>> On 13/03/2011 8

Re: [gmx-users] isopeptide bond

ease show us the [atoms] and [bonds] section for LYQ and GLYQ in your .top file. There were other points I made in an early email to which you've not responded, also. Mark 2011/3/13 Mark Abraham <mailto:mark.abra...@anu.edu.au>> On 13/03/2011 9:53 PM, Yulian Gavrilov wrote:

Re: [gmx-users] isopeptide bond

On 14/03/11, Yulian Gavrilov wrote: > Dear, Mark > > > > > > > > > > > > You asking about this (?): > > > > According to ffamber99.atp: > > > amber99_3414.01000; N sp2 > nitrogen in amide groups > > > amber99_

Re: [gmx-users] Energy calculation

On 14/03/11, "C.Y. Chang" wrote: > Hi, > > I try to calculate hydrogen bond (HB) energy. > The g_energy does not have this term. > And I find the g_hbond function in Gromacs. > But the HB energy calculation is not in g_hbond. > There's good reasons for this. How would you define the "HB ener

Re: [gmx-users] ffamber99.hdb

On 14/03/11, Yulian Gavrilov wrote: > > Dear gromacs users, > Please, can you explain the structure of ffamber99.hdb file > > For example, > LYN    7 > 1    1    H    N    -C    CA    > 1    5    HA    CA    N    CB    C    > > 2    6    HB    CB    CA    CG    > 2    6    HG    CG    CB 

Re: [gmx-users] Coulomb interactions

On 15/03/11, Swarnendu Tripathi wrote: > Hello everyone, > > In gromacs when the Coulomb interactions are calculated are they calculated > for the all atom pairs or only for the charged atoms pairs? > GROMACS notices atoms with zero charge and does not put them into lists scheduled for ev

Re: [gmx-users] Re: installation of gromacs (Dommert Florian)

On 15/03/11, Thomas Koller wrote: > Hello, > > I have installed Gromacs but if I want to open another terminal and run > another simulation it does not work. Do I need a further step? > See the link you were given last time, about getting access to GROMACS after installation. Mark -- gmx

Re: [gmx-users] isopeptide bond

he N should take its type from its current environment, not its historical one. Until your peptide bond resembles a backbone peptide in *all* particulars, it is not a well-modeled peptide bond. Mark > 2011/3/14 Mark Abraham > > > > > > > > > On 14

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