Re: [gmx-users] g_cluster for concoord output?

Hi Albert, pdb is mentioned valid input for both -f (trajectory) and -s (reference). So you can use the file you have for both: g_cluster -s disco.pdb -f disco.pdb [...] Cheers, Tsjerk On Tue, Apr 3, 2012 at 8:23 AM, Albert wrote: > Dear: > >    I've generated a disoc.pdb file by concoord and

AW: [gmx-users] the mdrun "-v"

Hey Acoot, The “–v” option simply means “verbose”, so mdrun outputs a bit more information (for example a nice finish time estimation) than it would do without “-v”. I doubt that giving a little bit more output to the console will influence the run time significantly. My advice: Just try it out

[gmx-users] g_cluster for concoord output?

Dear: I've generated a disoc.pdb file by concoord and does any one have any idea how to analyze it by Gromacs g_cluster? when I read the manual of g_cluter, it will require -f traj.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -s topol.tpr Input, Opt. Structur

[gmx-users] the mdrun "-v"

Dear All, For the function of mdrun. will you please introduce the time difference for the whole mdrun with or without "-v"? I suppose with "-v" will need some calculation time, but I am not sure whether the time spent is significant. Cheers, Acoot-- gmx-users mailing listgmx-users@gro

Re: [gmx-users] how to get a minimized structure pdb

On 03/04/12, balaji nagarajan wrote: > > > > > > > > > > Dear Users ! > > I have done a minimization for a tetrapeptide in a water box > > with conjugate gradient minimization of 1000 steps > > when I convert it to pdb as below > > > trjconv -f em.trr -o min.pdb -s em

[gmx-users] how to get a minimized structure pdb

Dear Users ! I have done a minimization for a tetrapeptide in a water box with conjugate gradient minimization of 1000 steps when I convert it to pdb as below trjconv -f em.trr -o min.pdb -s em.tpr << EOF 0 EOF the out put pdb has many structures as follo

[gmx-users] how to get a minimized structure pdb

Dear Users ! I have done a minimization for a tetrapeptide in a water box with conjugate gradient minimization of 1000 steps when I convert it to pdb as below trjconv -f em.trr -o min.pdb -s em.tpr << EOF 0 EOF the out put pdb has many structures as follo

[gmx-users] on the Umbrella Sampling on-line tutorial

Dear All, I planned to use the method introduced in the Umbrella Sampling on-line tutorial of Justin Lemkul (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html). But if a peptide is surrounded by a protein, which means the opening of the protein-com

Re: [gmx-users] Computing the total electrostatic energy (short range, 1-4, and Ewald) of an atom

On 03/04/12, Andrew DeYoung wrote: > Hi, > > Is it possible to compute the total electrostatic energy of an atom over > time? By "total," I mean including all of the terms (short range Coulomb, > 1-4 Coulomb, and Ewald), not just the short range Coulomb and 1-4 Coulomb. > > This question i

Re: [gmx-users] Re: how to g_select bound water molecules

OK. I have a protein "ab" and ligand "lig", and I want to select the bound water between them. So I used g_select -f trajout.xtc -s mdrun.tpr -n index.ndx -select '"boundwaters" resname SOL and within 0.4 of group "ab" and within 0.4 of group "lig"' -on boundwaters.ndx Then I can use the ndx file

[gmx-users] on the Umbrella Sampling on-line tutorial

Dear Acoot: I'll reply to general topics, not to the tutorial in particular. If the opening is not large enough to allow the peptide to exit, then the surrounding protein will need to change its conformation to permit unbinding. This can happen, but you need (a) to have sufficiently long s

[gmx-users] the mdrun -reprod in gromacs 4.5.5

Dear All, For gromcas 4.5.5 mdrun, is "-reprod (reproducibility)" is the default function or not? If not the default function, then how shod we input value for "-reprod" in order to get high reproducibility? The value should be "yes" or "no"? The on-line manual explanation on it makes me con

[gmx-users] Computing the total electrostatic energy (short range, 1-4, and Ewald) of an atom

Hi, Is it possible to compute the total electrostatic energy of an atom over time? By "total," I mean including all of the terms (short range Coulomb, 1-4 Coulomb, and Ewald), not just the short range Coulomb and 1-4 Coulomb. This question is somewhat related to a question I asked last week ( ht

[gmx-users] on the Umbrella Sampling on-line tutorial

Dear All, I planned to use the method introduced in the Umbrella Sampling on-line tutorial of Justin Lemkul (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html). But if a peptide is surrounded by a protein, which means the opening of the protein-comple

[gmx-users] How to compile the template.c when GMX is builded with cmake

Dear Users: I was previously able to compile template.c after I compiled gromacs with autoconf. I was unable to compile templae.c, however, I used cmake to compile gromacs. This is from gromacs-4.5.4. I tried "cmake ." in the template directory with no success: cmake .gpc-f102n084-$ cmake

RE: [gmx-users] Re: how to g_select bound water molecules

For future reference of others that may struggle with g_select, it would be a very good idea for you to put on the emailing list how you achieved it. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, P

RE: [gmx-users] a question related to the extending of md

Also, it is easy to join the two .edr files together, using eneconv However, it is probably better for you to simply start again and get the simulation to complete in one go. It should not take long to do. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Phar

[gmx-users] Re: how to g_select bound water molecules

Never mind. I got it. On Mon, Apr 2, 2012 at 4:20 PM, Yun Shi wrote: > Hello all, > > Can anyone tell me how to get in "help examples" in g_select by typing > some commands? > > Anyway, I want to select bound waters between my ligand and protein using > -select 'resname SOL & within 0.5 ...'. An

RE: [gmx-users] a question related to the extending of md

What .edr files are listed in the directory? Seems simply a case that the first section of the trajectory energy file has a separate file name to the last, i.e. the results weren't appended to the initial .edr file. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institu

[gmx-users] how to g_select bound water molecules

Hello all, Can anyone tell me how to get in "help examples" in g_select by typing some commands? Anyway, I want to select bound waters between my ligand and protein using -select 'resname SOL & within 0.5 ...'. Any idea? Thanks for any suggestion. Yun -- gmx-users mailing listgmx-users@gro

[gmx-users] a question related to the extending of md

     Dear All,   I am raning the 100 ps npt according to the on-line tutorial. For the computer reason it stops at about  less than50 ps.   Then I$ tpbconv -s npt.tpr -until 100 -o 100npt.tpr    mdrun -s 100npt.tpr -cpi npt.cpt -v   After completes I analyzee the g-energy. But xgrace shows for pr

Re: [gmx-users] ions error

Eduardo Oliveira wrote: OK, thanks for the info. I'm running GROMACS 4.5.5 Here is my genion command: genion_d -s sistema_stpr.tpr -o sistema_ion.gro -nname CL- -nn 3 -nq -1 -p sistema.top I chose the GROMOS force filed. Refer to the second paragraph of genion -h. -Justin --

Re: [gmx-users] ions error

Eduardo Oliveira wrote: Hi all, After a ran grompp_d in prepration for a Steepest Descente Minimizations with constraints i got the folowing error message: Fatal error: No such moleculetype CL- I don know for shure but i think that i forgot to modify some of the files with the numbers os

[gmx-users] ions error

Hi all, After a ran grompp_d in prepration for a Steepest Descente Minimizations with constraints i got the folowing error message: Fatal error: No such moleculetype CL- I don know for shure but i think that i forgot to modify some of the files with the numbers os CL- ions I've introduced int

Re: [gmx-users] em fatal error!

2 apr 2012 kl. 16.02 skrev lina: > On Mon, Apr 2, 2012 at 5:27 PM, ankita oindrila wrote: >> We are trying to do simulation of lysozyme in water. >> >> step with problem : energy minimization. >> >> command given: [root@localhost gromacs-4.0.5]# grompp -f minim.mdp -c >> 1AKI_solv_ions.gro -p

Re: [gmx-users] charges

On 2012-04-02 20:40, R.Perez Garcia wrote: Dear prof. van der Spoel, I know.. Dr. Alex de Vries is supervising me for my colloquium. Unfortunately (for me), they are very busy and (mainly) I am doing four months stage at Perugia universityv (It) which means I can not personally ask...so I prefer

Re: [gmx-users] charges

Dear prof. van der Spoel, I know.. Dr. Alex de Vries is supervising me for my colloquium. Unfortunately (for me), they are very busy and (mainly) I am doing four months stage at Perugia universityv (It) which means I can not personally ask...so I prefer to ask the list. Thank you for your answer

Re: [gmx-users] charges

On 2012-04-02 20:29, R.Perez Garcia wrote: Dear GROMACS users, I would like to place the charge more localized in the "bonds region" and not exactly in the atoms. Please let me know if you know there is a way to do this in GROMACS. Thank you in advance, R Yes, using virtual sites. There's an e

[gmx-users] charges

Dear GROMACS users, I would like to place the charge more localized in the "bonds region" and not exactly in the atoms. Please let me know if you know there is a way to do this in GROMACS. Thank you in advance, R -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

Re: [gmx-users] Editing of the existing system

By the way Today I've examined in vacuum minimisation outputs more carefully ( watching in vmd trr ) and found that conformation of the loops in the docked regions were changed after long CG minimisation. Then I've resolvate my system and add ions and run STEEP minimisation of that system. After

Re: [gmx-users] em fatal error!

On Mon, Apr 2, 2012 at 5:27 PM, ankita oindrila wrote: > We are trying to do simulation of lysozyme in water. > > step with problem : energy minimization. > > command given: [root@localhost gromacs-4.0.5]# grompp -f minim.mdp -c > 1AKI_solv_ions.gro -p topol.top -o em.tpr > >  

Re: [gmx-users] Re: Carbohydrate simulation: problem with the terminal atoms

khuchtumur wrote: Hi Justin, Thank you for writing this clarification. I'm still having a bit of a problem with the anomeric -OH group giving LINCS warnings during equilibration though. I am trying to parametrize a beta-lactose molecule in g53a6. Following are the steps I followed. 1) Draw

Re: [gmx-users] em fatal error!

Hi Ankita, >> command given: [root@localhost gromacs-4.0.5]# grompp -f minim.mdp -c >> 1AKI_solv_ions.gro -p topol.top -o em.tpr It is very unwise to run such things as root. By the way, if you follow a tutorial and refer to it, please send a link. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D

Re: [gmx-users] em fatal error!

Hi Ankita , The error is self-explanatory , and simple to interpret it. You check the Topology file and see the last line that showing added ions ... What was your genion COMMAND LINE Have a nice day Rama On Mon, Apr 2, 2012 at 3:19 PM, Erik Marklund wrote: >

[gmx-users] Re: Williams

Hello! What`s the meaning of the error "hi (0.00) <= lo (0.00)" that outputs g_cluster? Which the purpose of the option -rmsmin of g_cluster? Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://

Re: [gmx-users] Problems with simulation on multi-nodes cluster

On 2/04/2012 7:13 PM, James Starlight wrote: Mark, As I've told previously I have problems with the running simulation in multi-node mode. Yup, and my bet is you can't run any other software on multiple MPI nodes either, because your MPI system is not set up correctly, or maybe is too old.

Re: [gmx-users] Adding Born Radii for implicit solvent MD

On 2/04/2012 7:57 PM, german.erlenk...@pharmazie.uni-halle.de wrote: Dear Gromacs-Users, I want to do a MD with implicit solvent. During this I'll get the following erros. GB parameter(s) missing or negative for atom type 'ca' GB parameter(s) missing or negative

[gmx-users] Re: GPU support on GROMACS

Hi, > thought you can help with this... I'd appreciate if you kept future conversation on the mailing list. > The GROMACS website says Geforce GTX 560 Ti is supported. How about GTX 560? Yes, they are. All Fermi-class cards are supported. -- Szilárd > Thanks, > G > > -- > Gaurav Goel, PhD >

[gmx-users] Adding Born Radii for implicit solvent MD

Dear Gromacs-Users, I want to do a MD with implicit solvent. During this I'll get the following erros. GB parameter(s) missing or negative for atom type 'ca' GB parameter(s) missing or negative for atom type 'OS' GB parameter(s) missing or negativ

Re: [gmx-users] em fatal error!

2 apr 2012 kl. 11.27 skrev ankita oindrila: > We are trying to do simulation of lysozyme in water. > > step with problem : energy minimization. > > command given: [root@localhost gromacs-4.0.5]# grompp -f minim.mdp -c > 1AKI_solv_ions.gro -p topol.top -o em.tpr > > :-

[gmx-users] em fatal error!

*We are trying to do simulation of lysozyme in water.* step with problem : energy minimization. command given: *[root@localhost gromacs-4.0.5]# grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr* :-) G R O M A C S (-: Getting the Right Outp

Re: [gmx-users] Problems with simulation on multi-nodes cluster

Mark, As I've told previously I have problems with the running simulation in multi-node mode. I checked logs of such simulations and fond like this Will use 10 particle-particle and 6 PME only nodes This is a guess, check the performance at the end of the log file Using 6 separate PME nodes Thi

Re: [gmx-users] another g_tune_pme problem

On Apr 1, 2012, at 8:01 PM, Albert wrote: > Hello: > I am trying to test g_tune_pme in workstation by command: > > g_tune_pme_d -v -s md.tpr -o bm.trr -cpi md.cpt -cpo bm.cpt -g bm.log -launch > -nt 16 & > > but it stopped immediately with following logs. I complied gromacs with a -d > in e