Re: [gmx-users] openmm 3.0, opencl support

Valka ; Discussion list for GROMACS users Gesendet: 13:19 Montag, 25.April 2011 Betreff: Re: [gmx-users] openmm 3.0, opencl support Have you installed the CUDA Toolkit 4.0 ? I have never tried, just guessed. lina On Mon, Apr 25, 2011 at 9:17 AM, Claus Valka wrote: Hello, > &

[gmx-users] openmm 3.0, opencl support

Hello, I'm interested in knowing the level of development about gromacs supporting the opencl framework language. I have read the manual about gromacs 4.5.4 that says that opencl is going to be supported in future versions. Yet, in the openmm website, the new version of openmm (3.0 that is) is

[gmx-users] find with which mpi library /environment gromacs was compiled

Hello,I have a cluster with gromacs compiled. I would like to know which parallel environment I'm using. The version of operating system I use is centos version 5.1. When I open qmon and see the parallel environments that I have at my disposal I can see:lammpimpichorteI do know every command tha

RE: [gmx-users] compressibility tensor components, pressure coupling anisotropic PR, triclinic systems

Hello, thank you Mr Berk for your answers once again. Taking them as feedback and judging from my simulations, two more questions arise. I would be more than grateful if you could answer me the following: 1)you refer to an initial guess for the compressibility tensor of gromacs. As it was refer

RE: [gmx-users] compressibility tensor components, pressure coupling anisotropic PR, triclinic systems

Hello,I do have a crystal system. You refer to an initial guess. So if I understand correctly, it is a trial and error, if I do not have any data, this is what I can make out of. The part of the shear stress you are reffering I think that it is from experimental values? Now you say that : compre

[gmx-users] compressibility tensor components, pressure coupling anisotropic PR, triclinic systems

Hello, Searching first the gromacs mailing list I could not find an answer to the problem I face. I would like to know the vaules I have to give to the mdp file where it asks for compressibility. I have to conduct an NPT simulation using barostat Parrinello-Rahman. My pressure coupling should

RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3

r her querries. Thank you. Yours Sincerely, Nikos --- Claus Valka schrieb am Mi, 4.3.2009: Von: Claus Valka Betreff: RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3 An: "Discussion list for GROMACS users" Datum: Mittwoch, 4. März 2009, 16:12 H

RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3

omacs 4.0.3 To: gmx-users at gromacs.org --- Claus Valka schrieb am Mi, 4.3.2009: Hello, by charge groups you are referring to charge group number (cgnr) in the topology file. Every single atom in my chains belongs to a different charge group. My chains are polymer ones (identical) with 455 atoms

RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3

ct: WG: RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3 To: gmx-users@gromacs.org --- Claus Valka schrieb am Mi, 4.3.2009: Von: Claus Valka Betreff: RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3 An: "Berk Hess"

WG: RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3

--- Claus Valka schrieb am Mi, 4.3.2009: Von: Claus Valka Betreff: RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3 An: "Berk Hess" Datum: Mittwoch, 4. März 2009, 12:47 Dear Sir Berk, Thank you for your quick response. I simulate a system which has

RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3

Hello, the system I'm referring at is an already equilibrated one. Before, I had already made steepest descents. You are correct that I have non-bonded interactions at distances that are more than cut-off+table ext distance. I used to put table ext very bin in contrast to my box. My system bo

[gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3

Hello, this has to do with my personal experience of using Gromacs version 4.0.3. So this is not an official response. The story: While I was trying to run an NVT simulation in a monoclinic box I encountered the following problem: Fatal error: 25 of the 336080 bonded interactions could not be cal

RE: [gmx-users] gromacs-4.0.2, parallel performance in two quad core xeon machines

Hello,thank you for your answer. I just wondering though. How am I supposed to have a system with more than 9 atoms, while the gro file has a fixed format giving up to 5 digits in the number of atoms?  What else should I change in order to succeed better performance from my hardware if I can

[gmx-users] gromacs-4.0.2, parallel performance in two quad core xeon machines

Hello, we have built a cluster with nodes that are comprised by the following: dual core Intel(R) Xeon(R) CPU E3110 @ 3.00GHz. The memory of each node has 16Gb of memory. The switch that we use is a dell power connect model. Each node has a Gigabyte ethernet card. I tested the performance for

[gmx-users] ewald_rtol parameter question

Hello, I would like to ask you a (simple) clarification question: Reading the manual and equations 4.158 up to 4.160 there is a convergence parameter b (with hellenic letters β). I would like to ask you whether this parameter is the same as the ewald_rtol that I come accross in the manual. If it

[gmx-users] ewald_rtol parameter question

Hello,I would like to ask you a (simple) clarification question:Reading the manual and equations 4.158 up to 4.160 there is a convergence parameter b (with hellenic letters β).I would like to ask you whether this parameter is the same as the ewald_rtol that I come accross in the manual. If it is

[gmx-users] infinite polymer crystals at gromacs 4.x.x

Hello,back in gromacs versions 3.x.x there was the ability to simulate (polymer) crystals by enabling the option pbc = full in the mdp file.That way someone was avoiding the inconsistent shifts message and was able to simulate infinite systems.My question is: now in gromacs versions 4.0 and on,

Re: [gmx-users] Hildebrand's solubility parameter

Von: David van der Spoel <[EMAIL PROTECTED]> Betreff: Re: [gmx-users] Hildebrand's solubility parameter An: "Discussion list for GROMACS users" Datum: Dienstag, 2. Dezember 2008, 16:48 Claus Valka wrote: > Hello, > > could you tell me if it is possible with gromacs to

[gmx-users] Hildebrand's solubility parameter

Hello, could you tell me if it is possible with gromacs to calculate the Hildebrand's solubility parameter?  Thank you, Nikos ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Ple

[gmx-users] Re: grompp NOTE mdp file concerning steps

s An: [EMAIL PROTECTED], "Discussion list for GROMACS users" Datum: Mittwoch, 12. November 2008, 21:45 Hi Nikos, You mention it raises a note. What happens to the .tpr file? Can you look for nsteps in the output from gmxdump? Cheers, Tsjerk On Wed, Nov 12, 2008 at 2:45 PM, Claus Valka &l

[gmx-users] parallelization error? gromacs-4.0.2

Hello, I tried from the beginning to test gromacs-4.0.2 with a monoclinic system on 8 processors (one two quad core machine). The skew errors seem to be gone, yet other errors appeared. Now after a successful md, taking the output and trying to do annealing I get the following error: Fatal er

RE: [gmx-users] gromacs 4.0.2 error in continuation to triclinic skew error

Hello, the run didn't even start and I got this: Initializing Domain Decomposition on 8 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Minimum cell size due to bonded interactions: 1.000 nm Scaling the initial minimum size with 1/0.8 (option -dds)

RE: [gmx-users] gromacs 4.0.2 error in continuation to triclinic skew error

Hello, thank you for all your responses up to now. The thing is getting much more clearer. Yet, as far as the distance is concerned, this is a little bit worrying, because I have bonded interactions no more than 0.154 nm away. So a distance more than a whole nm I think that should be very long

[gmx-users] gromacs 4.0.2 error in continuation to triclinic skew error

Hello, (I remind you that my initial system is a monoclinic crystal, which is a sub categorie to triclinic boxes) compiling gromacs 4.0.2 with fftw3.2 and having the skew problem, now even in less steps than before, I face this: Not all bonded interactions have been properly assigned to the do

RE: [gmx-users] error: triclinic skew factor - number of DD cells

Hello, when I start the simulation my box vectors are the following : 16.89660   2.61581   2.07800   0.0   0.0  -0.43665   0.0   0.0   0.0 and with the command (the final written step was at 40487): trjconv -f traj.trr -dump 40487 -o out.gro I got these box vectors: 22.35607

[gmx-users] error: triclinic skew factor - number of DD cells

Hello, while I 'm executing an md run I came accross this error: Fatal error: The X-size of the box (22.541477) times the triclinic skew factor (0.317120) is smaller than the number of DD cells (8) times the smallest allowed cell size (0.895000) My system is monoclinic (sub-categorie to triclini

[gmx-users] Re: grompp NOTE mdp file concerning steps

Hello, searching further the issue, I realized that no more than 32299167 number of steps can be used. In case someone uses more, the note I describe makes its appearance. Is this a new limit? Regards, Nikos --- Claus Valka <[EMAIL PROTECTED]> schrieb am Mi, 12.11.2008: Von: Claus

[gmx-users] grompp NOTE mdp file concerning steps

Hello, I'm using gromacs version 4.0 and when I type : grompp -f file.mdp -c file.gro -p topol.top I get this note: NOTE 1 [file file.mdp, line unknown]: and nothing else. I checked my mdp file and I noticed than when I give 5000 steps I get this error (steps with more than 7 digits). If e

Re: [gmx-users] gromacs-4.0 error in grompp

ot;Discussion list for GROMACS users" Datum: Freitag, 17. Oktober 2008, 18:30 Claus Valka wrote: > Hello, > > While I'm trying to use the grompp command I get this error : > > Program grompp, VERSION 4.0 > Source code file: topio.c, line: 415 > > Fatal error:

[gmx-users] tables.xvg warning - error

Hello, In previous versions I do not get that error. My potential uses tables for non bonded intermolecular interactions. In gromacs-4.0 I get the following: WARNING: For the 1131 non-zero entries for table 1 in table_CGAC_CGCNZ.xvg the forces deviate on average 222% from minus the numerical d

[gmx-users] gromacs-4.0 error in grompp

Hello, While I'm trying to use the grompp command I get this error : Program grompp, VERSION 4.0 Source code file: topio.c, line: 415 Fatal error: Syntax error - File topol.top, line 4 Last line read: ' [ system ]' Invalid order for directive system I do not get this error in version 3.3.3 or 3

RE: [gmx-users] parallel run-more than one node / ci range checking error even applying the patch / parallel runs

Nikos --- Claus Valka <[EMAIL PROTECTED]> schrieb am Fr, 19.9.2008: Von: Claus Valka <[EMAIL PROTECTED]> Betreff: [gmx-users] ci range checking error even applying the patch / parallel runs An: gmx-users@gromacs.org Datum: Freitag, 19. September 2008, 16:24 Hello,after searching extens

[gmx-users] declaration of phi and psi dihedrals

Dear Sir or Madam,maybe it sounds a trivial question, yet how I define the phi and psi dihedrals in my topology. I have the section [ dihedrals ] in my topology, yet whenever I try to calculate them via g_chi I get that error :Fatal error: No dihedrals in your structure!and the g_rama command gi

[gmx-users] ci range checking error even applying the patch / parallel runs

Hello,after searching extensively the mailing lists I wasn' able to solve my problem. This has to do with running gromacs in parallel (more than one nodes) in a rocks cluster. I 'm able to run a simulation both in one or two processors in a dual core node, yet every time I try to use more than o

Re : [gmx-users] switch potential function gromacs 3.3.2

Dear Sir or Madam, For the version 3.3.2 the gromacs switch potential function is the following :  Elja1  = (4.d0*eps1*sig1**6) *    &    -(1.d0/r(i)**6) *    &     (1.d0 - 10.d0 * (r(i)-r1)**3 * 1.d0/(rc1-r1)**3 &       

[gmx-users] switch potential function gromacs 3.3.2

Hello,I would like to know the switching potential function.In the manual the potential function is Phi(r). Yet, this function has 1/nm**6 or 1/nm**12 units. So this potential should be multiplied by a factor. I supposed that this factor should be 6*4*epsilon*sigma**6 for the attractive part and

[gmx-users]Re: pairs potential

oding, probably there is a problem in one's topology. Regards, Nikos--- Claus Valka <[EMAIL PROTECTED]> schrieb am Mi, 9.7.2008: Von: Claus Valka <[EMAIL PROTECTED]> Betreff: [gmx-users] pairs potential An: gmx-users@gromacs.org Datum: Mittwoch, 9. Juli 2008, 12:01 Hello, I

[gmx-users] pairs potential

__ Gesendet von Yahoo! Mail. Dem pfiffigeren Posteingang. http://de.overview.mail.yahoo.com___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-use

[gmx-users] pairs potential

Hello, I would like to know the potential that the atoms under the pairs section are using. For that reason, I tried to test the most simple of systems, that is a two hydrogen system atom model. The sigma in my pairs section is 0.23160nm, yet I do not observe the pairs potential to be zero in

[gmx-users] tabulated potential both on pairs and non-bonded interactions / different cutoffs

Hello, trying to implement my force field into gromacs I have figured out that it is of vital importance to use diferrent cut-offs among different kind of atoms. I have 1-4 and 1-5 interactions with a set of epsilon and sigma parameters and the non bonded interactions (more than 4 bonds appart

[gmx-users] nrexcl 3 or 4 in combination with pairs 1-4

Dear Gromacs users, my system has both 1-4 and 1-5 interactions. I list all of them in pairs. According to nrexcl definition (gmx mail list), "setting nrexcl to 3 or 4 does NOT remove LJ-14". Yet, by switching this option from 3 to 4 I have a lot of differences not only in the non bonded but also

Re: [gmx-users] rvdw vs cut-off / different types of non bonded interactions

, I deeply appologize. Yours Sincerely, Nikos --- David van der Spoel <[EMAIL PROTECTED]> schrieb: > > > On Wed, 12 Dec 2007, Claus Valka wrote: > > > Dear Sir, > > > > I would try to be more precise. > > > > example1 mdp file: > > rlist =

Re: [gmx-users] rvdw vs cut-off / different types of non bonded interactions

different cutoffs for the different types of atoms I have. Am I correct? Yours Sincerely, Nikos --- Mark Abraham <[EMAIL PROTECTED]> schrieb: > Claus Valka wrote: > > Hello, > > > > > 3rd question: Which is the difference between the > > S(hort)R

[gmx-users] rvdw vs cut-off / different types of non bonded interactions

Hello, I have searched thoroughly the manual and the gmx list, yet with no avail. I'm trying to understand how I will be able to implement to gromacs my system which is complicated as far as the non bonded interactions are concerned. My system comprises three different types of atoms. The LJ int

Re: [gmx-users] create dihedrals' index giving the names of atoms from file

t frame) -type dihedral -od output.xvg Thank you once again, Nikos --- Mark Abraham <[EMAIL PROTECTED]> schrieb: > Claus Valka wrote: > > Dear gromacs users, > > > > my system comprises 16 polymer chains with 455 > atoms > > each. I want to calculate the dihedr

[gmx-users] create dihedrals' index giving the names of atoms from file

Dear gromacs users, my system comprises 16 polymer chains with 455 atoms each. I want to calculate the dihedral distribution for a number of dihedrals. I want to create an index file which will contain the global numbers (the third column of the gro file-concecutive number of atoms) of the atom-q

RE: [gmx-users] EM steep Total Energy

ate answer. Yours Sincerely, Nikos --- Berk Hess <[EMAIL PROTECTED]> schrieb: > > > > >From: Claus Valka <[EMAIL PROTECTED]> > >Reply-To: Discussion list for GROMACS users > > >To: gmx-users@gromacs.org > >Subject: [gmx-users] EM steep Total Energy &

[gmx-users] EM steep Total Energy

Dear GROMACS Developers, I have noticed that while doing Steep Energy Minimization, the Total Energy in the log file is zero. The potential energy is calculated as it should. In Conjugate Gradient or MD the total energy is calculated correctly. Is this a bug or a feature? I suppose that, under th

[gmx-users] monoclinic systems and pbc

Title : monoclinic polymeric crystal 12/12/06 Hello, I 'm trying to simulate a polymeric crystal in gromacs. I face some problems and I would appreciate your help. Sorry for the lengthy email, I am trying to be detailed, since I realized that I couldn't find much info about the use of mo

[gmx-users] rdf

Title : radial distribution function, 31.10.06 Hello, I am a new user of Gromacs (just started my Phd), and I'm trying to calculate the partial radial distibution functions for a system of polymer chains. In the topology file the system is described as