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 each

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

[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

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 :-) G R

[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

[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

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

[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

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

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] 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!

On Mon, Apr 2, 2012 at 5:27 PM, ankita oindrila oina...@gmail.com 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] 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.

[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

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

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

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] em fatal error!

2 apr 2012 kl. 16.02 skrev lina: On Mon, Apr 2, 2012 at 5:27 PM, ankita oindrila oina...@gmail.com 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

[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

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

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

[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

[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 list

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

[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 yunsh...@gmail.com 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

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

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,

[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 .

[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

[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 (

[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 confusing.

[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

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 to do

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

On 03/04/12, Andrew DeYoung adeyo...@andrew.cmu.edu 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.

[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

[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

[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

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

On 03/04/12, balaji nagarajan balaji_se...@hotmail.com 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