Re: [gmx-users] minimization

Morteza Khabiri wrote: Dear users I have a dimer protein which I want to minimized it..unfortunately the protein is in high energy level and before starting to minimize it explode. I already went through users email and also wiki gromacs and also I tried all the way like changing time step, chan

RE: [gmx-users] Energy Minimisation and Equilibration Problems

Have you managed to minimise a single molecule? Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When t

Re: [gmx-users] Energy Minimisation and Equilibration Problems

Nancy wrote: I ran the minimisation, and mdrun gave the following last few lines of output: == Step=19990, Dmax= 7.8e-06 nm, Epot= -7.14922e+04 Fmax= 3.19585e+04, atom= 2395 Step=19992, Dmax= 4.7e-06 nm, Epot= -7.14924e+04 Fmax= 8.72456e+03, atom= 2395 Step=19993,

Re: [gmx-users] Peptide drifting and non-natural amino acids

Kirill Bessonov wrote: I was giving today my poster presentation and one of profs from my department was very critical on the fact that my peptide is drifting or moving along the DMPC bilayer. Watch video of 100ns simulation here: He said that is unprobable, I want to know if this is some ki

Re: [gmx-users] Energy Minimisation and Equilibration Problems

I ran the minimisation, and mdrun gave the following last few lines of output: == Step=19990, Dmax= 7.8e-06 nm, Epot= -7.14922e+04 Fmax= 3.19585e+04, atom= 2395 Step=19992, Dmax= 4.7e-06 nm, Epot= -7.14924e+04 Fmax= 8.72456e+03, atom= 2395 Step=19993, Dmax= 5.6e-06

Re: [gmx-users] Error in PDB2GMX

sunny mishra wrote: Thats great. I am able to make now my 1A8G.itp file and also the CG structure of protein but now the other problem which is arising is to make the topol.top file and conf.gro file. When I am making this using the command...pdb2gmx -v -f 1A8G_CG.pdb -o conf.gro -p topol.top .

[gmx-users] RE: Peptide drifting and non-natural amino acids

Sorry the link: You see that peptide is moving from right to the left of the box http://www.youtube.com/watch?v=_6e4Rfl6Yrc ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive a

[gmx-users] Error in PDB2GMX

Thats great. I am able to make now my 1A8G.itp file and also the CG structure of protein but now the other problem which is arising is to make the topol.top file and conf.gro file. When I am making this using the command...pdb2gmx -v -f 1A8G_CG.pdb -o conf.gro -p topol.top ..it says choose the

[gmx-users] Peptide drifting and non-natural amino acids

I was giving today my poster presentation and one of profs from my department was very critical on the fact that my peptide is drifting or moving along the DMPC bilayer. Watch video of 100ns simulation here: He said that is unprobable, I want to know if this is some kind of artifact (i.e. system i

Re: [gmx-users] Error in PDB2GMX

sunny mishra wrote: Hi Justin, Thanks for the expedient reply. I referred MARTINI but after converting 1A8G.pdb to 1A8G_CG.pdb i.e. CG structure of protein I dnt know how to make the topol.top and conf.gro files for that and also I am not able to generate the posre.itp file with this CG struct

[gmx-users] Error in PDB2GMX

Hi Justin, Thanks for the expedient reply. I referred MARTINI but after converting 1A8G.pdb to 1A8G_CG.pdb i.e. CG structure of protein I dnt know how to make the topol.top and conf.gro files for that and also I am not able to generate the posre.itp file with this CG structure because it says the

Re: [gmx-users] Error in PDB2GMX

sunny mishra wrote: Hi, I am working on HIV-1 Protease with PDB ID 1A8G.pdb. I am trying to convert this protein structure to COARSE GRAINED protein structure and I am done with that but when I am trying to make the topology and conf.gro file from my CG structure of 1A8G.pdb using pdb2gmx it

[gmx-users] Error in PDB2GMX

Hi, I am working on HIV-1 Protease with PDB ID 1A8G.pdb. I am trying to convert this protein structure to COARSE GRAINED protein structure and I am done with that but when I am trying to make the topology and conf.gro file from my CG structure of 1A8G.pdb using pdb2gmx it gives me the FATAL ERROR

Re: [gmx-users] Very High Forces During Minimisation

Nancy wrote: I have tried 15,000 steps; I noticed that Fmax starts out at ~3.0e+03 and increases to ~1.2e+06 before coming down very slowly to ~5.0e+04. Additionally, letting the minimisation run for a long time gives me a "converged to machine precision, but not to Fmax < 10" message. A

[gmx-users] Re: Error in PDB2GMX

Please keep all Gromacs-related correspondence on the gmx-users list. As I have said dozens of times, I do not advertise myself as a private tutor, nor do I always have the right solutions. sunny mishra wrote: Dear Justin, I read your solutions always in the GROMACS discussion topics. I ha

Re: [gmx-users] Very High Forces During Minimisation

I have tried 15,000 steps; I noticed that Fmax starts out at ~3.0e+03 and increases to ~1.2e+06 before coming down very slowly to ~5.0e+04. Additionally, letting the minimisation run for a long time gives me a "converged to machine precision, but not to Fmax < 10" message. I am wondering why the

Re: [gmx-users] Energy Minimisation and Equilibration Problems

On Thursday, August 6, 2009 at 4:08:18 PM, Nancy wrote: > I have attempted to perform energy minimisation from scratch again, and these > are the > commands that I am using to do so: > > $ .../topolbuild1_2_1/src/topolbuild -n ethanediol -dir > .../topolbuild1_2_1/dat/gromacs -ff gmx53a6 >

Re: [gmx-users] Very High Forces During Minimisation

Nancy wrote: Note: the ethanediol.log file contains a section that has several lines with asterisks: Angles Force Field Results AngleAtomsforceangle method measured 1 H12- C1- H11 ** ** **109.403 Proba

[gmx-users] Very High Forces During Minimisation

Hello, I am trying to equilibrate and run MD on a system of solvated ethylene glycol (ethanediol). However I am running into numerous problems. First, I try to minimise the system. I start with an ethanediol.mol2 file which contains the structure of the molecule. $ .../topolbuild1_2_1/src/topo

RE: [gmx-users] Suggestions for 3D-monitor/glasses for visualizing GROMACS output

Suggest you have a look and search the VMD emailing lists. These sorts of visualisation discussions come up from time to time with people sharing their experiences. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal

[gmx-users] FEP problem with lambda perturbation 1 to 0.95

I am performing FEP do obtain the dimerization of a protein in membrane. The lambda intervals i am using are 0.05 for each window. After that I rerun each lambda .trr perturbing the system (plus)0.05 and (minus)0.05 lambda value. Then with g-energy I obtain the deltaG for each delta lambda. Well, I

Re: [gmx-users] Re: Difficulty running test particle insertion calculation

The integrator in your .mdp file is "md" when it should be "tpi." -Justin Jack Roberts wrote: I have now also tried defining separate energygrps in the input file thinking this was possibly a energy/charge group related issue, but I am still having no success. I still receive the same error.

[gmx-users] Re: Difficulty running test particle insertion calculation

I have now also tried defining separate energygrps in the input file thinking this was possibly a energy/charge group related issue, but I am still having no success. I still receive the same error. Any constructive responses would be helpful at this point. On Thu, Aug 6, 2009 at 12:04 PM, aeBie

Re: [gmx-users] pairing error

mohit kumar wrote: but i dnt find any 'type' column in my topology file..the grompp programm with this top file works gud in 3.3 version..im having 4.0.5 version..is that can be issue?? shud i try in 3.3 version This may be some new error-checking mechanism introduced in version 4.0. In

[gmx-users] simple question about umbrella pulling

Folks -- Reading Section 7.3.21 "COM pulling" in the GROMACS 4.0 manual, I don't quite see how to specify a nonzero minimum distance for an umbrella potential. I see that pull = umbrella pullgroup0 = ... pullgroup1 = ... pull_k1 = ... ; sets the force constant

Re: [gmx-users] pairing error

but i dnt find any 'type' column in my topology file..the grompp programm with this top file works gud in 3.3 version..im having 4.0.5 version..is that can be issue?? shud i try in 3.3 version On Thu, Aug 6, 2009 at 2:48 PM, Justin A. Lemkul wrote: > > > mohit kumar wrote: > >> im running energy

Re: [gmx-users] Energy Minimisation and Equilibration Problems

I have attempted to perform energy minimisation from scratch again, and these are the commands that I am using to do so: $ .../topolbuild1_2_1/src/topolbuild -n ethanediol -dir .../topolbuild1_2_1/dat/gromacs -ff gmx53a6 which generates the files: ethanediol.gro ethanediol.log ethanediolMOL.mol2

RE: [gmx-users] Re: Free Energy Calculation

A question to the answer below: If the Berendsen barostat does not sample correctly the distribution of pressures then what guarantees that the the volume/density is correct at the end of the equilibration phase when the user is advised to switch to NVT? Peter Nagy The University of Toledo

Re: [gmx-users] pairing error

mohit kumar wrote: im running energy minimization for POPC bilayer but its showing error which i cant figure out -- --- Program grompp, VERSION 4.0.5 Source code file: topdirs.c, line: 99 Fatal error: Invalid pairs type 0 what does this pa

[gmx-users] pairing error

im running energy minimization for POPC bilayer but its showing error which i cant figure out -- --- Program grompp, VERSION 4.0.5 Source code file: topdirs.c, line: 99 Fatal error: Invalid pairs type 0 what does this pair type mean and how can

[gmx-users] minimization

Dear users I have a dimer protein which I want to minimized it..unfortunately the protein is in high energy level and before starting to minimize it explode. I already went through users email and also wiki gromacs and also I tried all the way like changing time step, change coulomb type ,... but

Re: [gmx-users] Both atom and residue type four letters . . .

Marc Charendoff wrote: Fatal error: Atom ZN2+ in residue ZN2+ 1 not found in rtp entry with 1 atoms while sorting atoms This means your .pdb file format is fine. Unfortunately (and I missed this the first time, too), the only thing wrong is the atom name. In ffG43a1.rtp: [ ZN2+ ] [ a

[gmx-users] Re: Free Energy Calculation

Hi, Sorry for the delay answering. These questions are better put on the GROMACS users list. 1) Yes -- the Berendsen barostat does not sample the correct distribution of pressures. 2) Regenerating velocities is fine for a couple of reasons: (a) we are after thermodynamics, not dynamics, a

Re: [gmx-users] Energy Minimisation and Equilibration Problems

On Thursday, August 6, 2009 at 11:58:20 AM, Nancy wrote: > The energies simply do not seem to come down any further within several > thousand steps. > > I start with a .mol2 file which contains the structure of ethylene glycol (ethanediol). > These are the commands that I use to set up and run

[gmx-users] Both atom and residue type four letters . . .

Hello,   Well, I have tried a couple of permuatations and I seem to clear up one problem only to get another. Any hints as to what to do when both atomtype AND residuetype each are four letter designates? Not seeing anything in the manual.   Thanks again.     Back Off! I just backed up posre_A.it

[gmx-users] Suggestions for 3D-monitor/glasses for visualizing GROMACS output

Dear list, I know this might be a bit off topic. Sorry in advance. We have a grant app for upgrading our CRAY and I wanted to include the latest 3D visualization workstation to visualize my GROMACS trajectories. Any suggestions? LCD or CRT? Shutter glasses, no glasses? I am very new to this and

Re: [gmx-users] Energy Minimisation and Equilibration Problems

Nancy wrote: I then proceed to enlarge the box and solvate the molecule: $ editconf -f ethanediol.gro -o ethanediol_box.gro -box 5 5 5 $ genbox -cp ethanediol_box.gro -cs spc216.gro -o ethanediol_box.gro -p ethanediol.top -shell 1 So, instead of filling the box, you are simply specif

[gmx-users] Difficulty running test particle insertion calculation

I am attempting to run a test particle insertion calculation of Argon in SPC/E water using GROMACS 4.0.3. Here is what I have done so far: 1. Generated a .trr file with a simulation of 512 SPC/E water molecules 2. Added an Argon atom to the SPC/E .gro and .top files 3. Used grompp to gen

Re: [gmx-users] Energy Minimisation and Equilibration Problems

The energies simply do not seem to come down any further within several thousand steps. I start with a .mol2 file which contains the structure of ethylene glycol (ethanediol). These are the commands that I use to set up and run the minimisation: $ .../topolbuild1_2_1/src/topolbuild -n ethanediol

Re: [gmx-users] Install gromacs333 with plumed110

This question is more appropriate to the plumed-users forum. Giovanni On Thu, Aug 6, 2009 at 4:42 PM, osmair oliveira wrote: > Hi, >  I am trying to install gromacs 3.3.3 with plumed 1.1.0 with the following > commands: > $ export plumedir=/home/osmair/programs/PLUMED-1.1.0 > $ CC=gcc CXX=g++ ./c

[gmx-users] Install gromacs333 with plumed110

Hi, I am trying to install gromacs 3.3.3 with plumed 1.1.0 with the following commands: $ export plumedir=/home/osmair/programs/PLUMED-1.1.0 $ CC=gcc CXX=g++ ./configure --enable-double --program-suffix=_plumed --enable-fortran --enable-mpi CPPFLAGS=-I/home/osmair/programs/fftw-3.0.1/include

Re: [gmx-users] Energy Minimisation and Equilibration Problems

On Wednesday, August 5, 2009 at 6:03:51 PM, Nancy wrote: > I am trying to run equilibration on my solvated ethylene glycol (ethanediol) system. I started > with an ethanediol mol2 file from which topolbuild generated various files. I used editconf > to enlarge to box of the "ethanediol.gro" file

Re: [gmx-users] g_order warning message

Andrei Neamtu wrote: Dear Justin, thank you for your reply. I am not trying to obtain the tethraedrality order parameter. I want to use the g_order on a linear flexible molecule grafted to the surface of the bilayer. I think that the usual united atom order parameter (the component on the dir

RE: [gmx-users] pull code problem

Hi, First, please switch to 4.0.5, I have put several fixes in the pull code in the 4.0 minor releases. You did not specify pull_init1, nor pull_start, this means you start pulling at a distance of 0, which means the center of the bilayer. Setting pull_start = yes should fix your problem. Berk

[gmx-users] Model(l)ing'09 in Erlangen, Germany: Registration Open Until August 31st

Dear List Subscribers, A Molecular Graphics and Modelling Society (MGMS) International Meeting will take place in Erlangen, Germany from September 7th (registration and mixer) to 11th 2009. The meeting will be preceded by the annual Molecular Modelling Workshop organised by the MGMS German Secti

Re: [gmx-users] g_order warning message

Dear Justin, thank you for your reply. I am not trying to obtain the tethraedrality order parameter. I want to use the g_order on a linear flexible molecule grafted to the surface of the bilayer. I think that the usual united atom order parameter (the component on the direction perpendicular to t