Re: [gmx-users] problems when installing gromacs 4.5.3 or 4.5.4 with GPU's

Thanks Szilárd for your fast mail, but it seems that is still failing and don't appears any new error. With BUILD_SHARED_LIBS flag it seems that it pass the library error but I receive a similar error with the executable (see attached file) mdrun-gpu, but this executable exist in other directo

Re: [gmx-users] oligoglycines

Hi Nisha, For building you can also use pymol if you have it installed. On the command line you can issue: pymol -qcd 'editor.build_peptide("GGG");cmd.save("triglycine.pdb","not hydro")' Hope it helps, Tsjerk On Mon, Mar 28, 2011 at 6:05 PM, wrote: > Hello, > >   I want to simulate n-glycine

Re: [gmx-users] PSF files from .top to .psf

Mark Abraham wrote: On 29/03/2011 4:06 AM, Donovan B.T. wrote: Hi All I'm trying to measure some dipole moments in VMD using "measure dipole", but am having trouble with the .psf file format. I'm not sure that the conversion tool [top2psf] is coping with the .top file and its three .itn in

Re: [gmx-users] PSF files from .top to .psf

On 29/03/2011 4:06 AM, Donovan B.T. wrote: Hi All I'm trying to measure some dipole moments in VMD using "measure dipole", but am having trouble with the .psf file format. I'm not sure that the conversion tool [top2psf] is coping with the .top file and its three .itn include files. I have trie

Re: [gmx-users] Re: mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family

On 29/03/2011 12:17 AM, sa wrote: OK, Pr van der Spoel, So what is the correct way to obtain LJ C6 and C12 values given in the [ atomtypes ] and in the [ nonbond_types] sections of ffnonbonded.itp if I have only the sigma and epsilon values. If understand well [ atomtypes ] section giv

Re: [gmx-users] Re: Resplica exchange with solute tempering (REST)

On 29/03/2011 4:54 AM, Sai Pooja wrote: There was a typo in the mail: E_protein-protein = Potential - E_water-water - E_protein-water On Mon, Mar 28, 2011 at 11:55 AM, Sai Pooja > wrote: Hi, I have tried to implement a variant of Replica exchange called

Re: [gmx-users] Placing ions at a required distance

shivangi nangia wrote: Hi again, I did not quite understand the suggestion. I have successfully added Li+ ions in my simulation box using genion. I am confused about how to place Li+ ions using editconf. Are these ions simply going to be part of the bulk solution? If so, use genion. Manu

Re: [gmx-users] re: Gromos96 43A1

Frank Neuhaus wrote: Gmx-users, I am in the process of deciding on a force field library for a MD simulation. In reading Lemkul et al I get the impression that GROMOS96 43A1 is probably the one to use. I am trying to do a simulation Hopefully you have not gotten the impression from our wo

Re: [gmx-users] Placing ions at a required distance

Hi again, I did not quite understand the suggestion. I have successfully added Li+ ions in my simulation box using genion. I am confused about how to place Li+ ions using editconf. Will I have to create a .gro and .itp file and add it like a solute ? Thanks, Shivangi On Mon, Mar 28, 2011 at 3

Re: [gmx-users] implicit solvent model: formulation of non-polar free energy

Hi! I know about this difference. The only reason for it is that, when I first started with this I used Tinker as a reference implementation, which has the 6-th power in the code. The differences should be small, though. The non-polar part only amounts to a few percent of the total force anywa

Re: [gmx-users] Is there still interest in rigid-body simulation?

On 27/03/11 23:02, Adam Herbst wrote: Hi all, I have seen a few posts on gmx-users indicating a desire to treat certain atom groups as rigid bodies in MD simulations. I just started implementing this, and so far I have it working for translational forces (not rotation, though this should be simp

[gmx-users] re: Gromos96 43A1

Gmx-users, I am in the process of deciding on a force field library for a MD simulation. In reading Lemkul et al I get the impression that GROMOS96 43A1 is probably the one to use. I am trying to do a simulation with a ligase that binds ADP, 2Mg, D-alanine and D-lactate. From these authors, I

Re: [gmx-users] problems when installing gromacs 4.5.3 or 4.5.4 with GPU's

Hi Jordi, I've never seen this error or anything similar, but I can give you hints. The CMake build system first generates binaries in the build directory which are also runnable from there (are linked against libs located in the build three). When you do a "make install[-mdrun]", howerver, these

Re: [gmx-users] Placing ions at a required distance

shivangi nangia wrote: Hello, I am a new gromacs user. I want to place Li+ ions at a required distance from the polypeptide ( which is at the centre of a box of water) I searched through the archive and the manual if there is a way/provision to do this, but could not. Is there a way?

[gmx-users] implicit solvent model: formulation of non-polar free energy

Hi everyone, I am going through the source code for the GB calculation part of gromacs, and found the following code in "src/mdlib/genborn.c" : in the function "real calc_gb_nonpolar()" rai = top->atomtypes.gb_radius[md->typeA[ai]]; rbi_inv = fr->invsqrta[ai]; rbi_inv2 = rbi_inv * rbi_in

[gmx-users] Placing ions at a required distance

Hello, I am a new gromacs user. I want to place Li+ ions at a required distance from the polypeptide ( which is at the centre of a box of water) I searched through the archive and the manual if there is a way/provision to do this, but could not. Is there a way? Please guide. Thanks, Shivangi

[gmx-users] Re: Resplica exchange with solute tempering (REST)

There was a typo in the mail: E_protein-protein = Potential - E_water-water - E_protein-water On Mon, Mar 28, 2011 at 11:55 AM, Sai Pooja wrote: > Hi, > > I have tried to implement a variant of Replica exchange called REST using > gromacs. In REST, the potential energy is scaled in the following

[gmx-users] PSF files from .top to .psf

Hi All I'm trying to measure some dipole moments in VMD using "measure dipole", but am having trouble with the .psf file format. I'm not sure that the conversion tool [top2psf] is coping with the .top file and its three .itn include files. I have tried numerous work around's for include files [

Re: [gmx-users] oligoglycines

Thanks Justin! Nisha P Quoting "Justin A. Lemkul" : nishap.pa...@utoronto.ca wrote: Hello, I want to simulate n-glycines (diglycine, triglycine..etc) I tried to get the structure from PRODRG, but the program adds H's on the N-terminal instead of on C- terminal. Is there another pr

Re: [gmx-users] oligoglycines

nishap.pa...@utoronto.ca wrote: Hello, I want to simulate n-glycines (diglycine, triglycine..etc) I tried to get the structure from PRODRG, but the program adds H's on the N-terminal instead of on C- terminal. Is there another program I could use, or a site where I could get the structur

Re: [gmx-users] Gromacs for carbohydrates

Geethu Issac wrote: /Hello Users,/ /I am doing simulation of gm2 ganglioside using GROMACS.Can anyone please help me in knowing the parameterization of carbohydrates and also any tutorial for simulation of carbohydrates using GROMACS./ The parameterization methodology depends on the force f

[gmx-users] oligoglycines

Hello, I want to simulate n-glycines (diglycine, triglycine..etc) I tried to get the structure from PRODRG, but the program adds H's on the N-terminal instead of on C- terminal. Is there another program I could use, or a site where I could get the structure of oligoglycines? For exampl

[gmx-users] Resplica exchange with solute tempering (REST)

Hi, I have tried to implement a variant of Replica exchange called REST using gromacs. In REST, the potential energy is scaled in the following manner: For the nth replica: E_n = E_protein-protein + a_n * E_protein-water + b_n * E_water-water I used tables to implement this. Separate tables for

[gmx-users] Gromacs for carbohydrates

*Hello Users,* *I am doing simulation of gm2 ganglioside using GROMACS.Can anyone please help me in knowing the parameterization of carbohydrates and also any tutorial for simulation of carbohydrates using GROMACS.* *Thanks in advance* -- *Geethu Issac* * * -- gmx-users mailing listgmx-us

Re: [gmx-users] No DD grid found

Dear all, Really appreciate the fast and very clear reply. Now I know how to overcome this issue. Best, André On 28-03-2011 13:25, Mark Abraham wrote: On 28/03/2011 10:37 PM, André Ferreira wrote: Dear all, I am having some problems with some molecules that I am currently simulating. I go

[gmx-users] Re: Is there still interest in rigid-body simulation?

Ignacio, I would be very interested in a rigid body capability. On 3/28/2011 5:45 AM, gmx-users-requ...@gromacs.org wrote: Is there still interest in rigid-body simulation? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

Re: [gmx-users] Re: mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family

> > OK, Pr van der Spoel, > So what is the correct way to obtain LJ C6 and C12 values given in the [ atomtypes ] and in the [ nonbond_types] sections of ffnonbonded.itp if I have only the sigma and epsilon values. If understand well [ atomtypes ] section give the comb-rules for the atom with itse

Re: [gmx-users] flexible spc water model

On 28/03/2011 11:29 PM, Nilesh Dhumal wrote: I want to calculate the vibrational spectra of water by fourier transfom of velocity autocorrelation function. TO study stretching and bending vibration I have to use spc flexible water model. You probably should to use a flexible water model, but ma

Re: [gmx-users] flexible spc water model

Nilesh Dhumal wrote: I want to calculate the vibrational spectra of water by fourier transfom of velocity autocorrelation function. TO study stretching and bending vibration I have to use spc flexible water model. Well, hopefully someone has proven that this should be possible. SPC was des

Re: [gmx-users] mdrun

On 28/03/2011 7:06 PM, michael zhenin wrote: Dear all, I am trying to run dynamics (mdrun) on GROMACS 4.5.3 in parallel on 8 processors, but it crashes after a while and refuses to reach to the end. The error note that pops out is: 1 particles communicated to PME node 4 are more than 2/3 times

Re: [gmx-users] flexible spc water model

I want to calculate the vibrational spectra of water by fourier transfom of velocity autocorrelation function. TO study stretching and bending vibration I have to use spc flexible water model. Nilesh On Fri, March 25, 2011 12:02 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Hello,

[gmx-users] Re: gmx-users Digest, Vol 83, Issue 196

/attachments/20110328/33c5a2e5/attachment-0001.html > > -- > > Message: 3 > Date: Mon, 28 Mar 2011 07:27:11 -0400 > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] mathematical expression to obtain the C6 and >C12 LJ terms for th

Re: [gmx-users] No DD grid found

On 28/03/2011 10:37 PM, André Ferreira wrote: Dear all, I am having some problems with some molecules that I am currently simulating. I got simulation box that is constituted by 100 oligomer molecules (190 atoms each), in a cubic box with 7 nm side (50K). Since the molecule is quite long I am

Re: [gmx-users] No DD grid found

André Ferreira wrote: Dear all, I am having some problems with some molecules that I am currently simulating. I got simulation box that is constituted by 100 oligomer molecules (190 atoms each), in a cubic box with 7 nm side (50K). Since the molecule is quite long I am using a rcoulomb of 2

Re: [gmx-users] Re: mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family

On 2011-03-28 14.07, sa wrote: Sorry I forget to say in my previous mail that the values obtained by g_sigeps_mpi are not similar to the values given in the GROMOS53A6 ffnonbonded.itp for the OM atom. OM8 0.000 0.000 A 0.0022619536 7.4149321e-07 Difficult to compare this way

Re: [gmx-users] Re: mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family

sa wrote: Sorry I forget to say in my previous mail that the values obtained by g_sigeps_mpi are not similar to the values given in the GROMOS53A6 ffnonbonded.itp for the OM atom. I understand that. Everything I said an hour ago (http://lists.gromacs.org/pipermail/gmx-users/2011-March/059

Re: [gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral

On 28/03/2011 8:45 PM, maria goranovic wrote: That would mean that a new residue type will not be required? I just need the correct input D-coordinates? Try it, before asking about it :-) I said "I suspect you do not need to change anything about the topology", but I haven't actually done any

[gmx-users] No DD grid found

Dear all, I am having some problems with some molecules that I am currently simulating. I got simulation box that is constituted by 100 oligomer molecules (190 atoms each), in a cubic box with 7 nm side (50K). Since the molecule is quite long I am using a rcoulomb of 2.8 nm and rvdw of 3.4 nm

[gmx-users] Re: mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family

Sorry I forget to say in my previous mail that the values obtained by g_sigeps_mpi are not similar to the values given in the GROMOS53A6 ffnonbonded.itp for the OM atom. OM8 0.000 0.000 A 0.0022619536 7.4149321e-07 So your advices are welcome. SA 2011/3/28 sa > Thank you

Re: [gmx-users] mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family

sa wrote: Thank you Justin for your response I have tried g_sigeps with the OM type LJ values (sigma (nm) = 0.3137 and epsilon (kj/mol) = 1.2231 given in Poger et al. Paper (JCC Vol 31, 6, 1117) as an example. Unfortunately i can't retrieve the C6 and C12 values given for the s

[gmx-users] mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family

> > Thank you Justin for your response > I have tried g_sigeps with the OM type LJ values (sigma (nm) = 0.3137 and epsilon (kj/mol) = 1.2231 given in Poger et al. Paper (JCC Vol 31, 6, 1117) as an example. Unfortunately i can't retrieve the C6 and C12 values given for the same in the GROMOS

[gmx-users] problems when installing gromacs 4.5.3 or 4.5.4 with GPU's

Hi, I'm compiling gromacs with gcc compiler (v 4.3.2), cmake (2.8.3) and OpenMM 2.0 in a SLES 11.0 Linux. I follow the instructions in the page and it seems that the compilation goes fine. gpu01:/scratch/jingles/gcc/gromacs-4.5.3 # ls -ltra src/kernel/mdrun-gpu -rwxr-xr-x 1 root root 518294

Re: [gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral

That would mean that a new residue type will not be required? I just need the correct input D-coordinates? On Sat, Mar 26, 2011 at 2:02 AM, Mark Abraham wrote: > On 26/03/2011 2:27 AM, maria goranovic wrote: > > Yes, that would be the correct way to do this. I was hoping to take a > shorter rout

Re: [gmx-users] GROMACS 4.5 and MARTINI Force Field Installation

You can use any GROMACS version to run a simulation with the Martini Force field. IT is only if you want to back-map your system to an atomistic resolution that you'll have to use the gmx331 modified version. On Mar 27, 2011, at 8:25 PM, Edroaldo Lummertz da Rocha wrote: Dear GROMACS users, I

Re: [gmx-users] Is there still interest in rigid-body simulation?

From: Adam Herbst To: Discussion list for GROMACS users Sent: Mon, 28 March, 2011 0:02:17 Subject: [gmx-users] Is there still interest in rigid-body simulation? > Hi all, > I have seen a few posts on gmx-users indicating a desire to treat certain > atom > groups as rigid bodies in MD simulati

[gmx-users] mdrun

Dear all, I am trying to run dynamics (mdrun) on GROMACS 4.5.3 in parallel on 8 processors, but it crashes after a while and refuses to reach to the end. The error note that pops out is: 1 particles communicated to PME node 4 are more than 2/3 times the cut-off >> out of the domain decomposition