[gmx-users] Pressure coupling appears to produce errors on the P655+ aix 5.2

Hi, All, I would like to thank Carsten Kutzner, Erik Lindahl, and David van der Spoel for their advise with my previous problem with not getting any data with mdrun. It turned out to be due to the fourier spacing and the PME order. In addition, David van der Spoel's suggestion of using a water s

[gmx-users] Question about phospholipid monolayer on a water/air interface

Hi My name is Sergio Garay, and I'm working on a simulation of a phospholipid monolayer on a water/air interface. To mimic that system I have constructed a rectangular box with a thick layer of water at the center, two monolayer of lipids (with their polar heads pointing toward water) at each

[gmx-users] Re: parallel in duals?

Hi David Fortunatelly, I don't have to buy now... But I have to upgrade only the processor (that's the problem: locked in the sk 939 by now) by the end of the year. Full new computers only next year (seems to be good, anyway), with all new techs (dual procs mb for normal people, 4x cores, etc.).

Re: [gmx-users] Long range interaction energy of charged particles with PME - GMX 3.3.1

David, Just for your information, Erik and I are writing this up in the context of free energy calculations. We could probably upload a draft to arXiv. Please do! This is something we're very interested in; if there is some way to properly handle these right now, we will probably use it. Tha

Re: [gmx-users] Long range interaction energy of charged particles with PME - GMX 3.3.1

I was not accurate. E(LR) is the total PME energy, and the rest can be extracted by neutralising selected groups. So the binding energy can calculated from: E(LR)-E(sol-sol)- E(ligand-ligand)- E(protein-protein)-E(solvent-ligand)-E(solvent-protein), where e.g. E(sol-sol) can be calculated w

Re: [gmx-users] Deshuffling atoms vs. residues

Jerome Henin wrote: On Tuesday 01 August 2006 10:08, David van der Spoel wrote: Jerome Henin wrote: Okay, now I have a partial answer to my own question. Apparently, when using the -sort and -shuffle options, the indexfile written by grompp undoes the shuffling, but not the sorting, so to spe

[gmx-users] how to calculate prot-ligand interaction energy

Hi, I have recently run a MD in gromacs 3.3.1. I would like to calculate the interaction energy between protein and the ligand which i have used. If I use the options LJ-SR or LJ-LR the program is considering it as LJ-14 and giving the same result. Many thanks in advance. Rajaram Do you Yah

Re: [gmx-users] Re: parallel in duals?

Jones de Andrade wrote: Hi David. Well, it wasn't me who did the test. :) My problem is that I cannot try it; I rather have to choose what to buy: extra cores, or extra clock frequency? search the mailing list for woodcrest and you will find Florian Haberl's benchmarks. If you have to buy n

[gmx-users] Re: parallel in duals?

Hi David. Well, it wasn't me who did the test. :) My problem is that I cannot try it; I rather have to choose what to buy: extra cores, or extra clock frequency? Does anybody have an advise on this subject? Thank you all... Jones On 8/1/06, David van der Spoel <[EMAIL PROTECTED]> wrote: Jon

Re: [gmx-users] Toplogy file FAD and ADP!

Samuel Silva Pita wrote: Dear Gmxers, i've trying to develop the topology files for FAD and ADP since the GMX 3.3.1 does not have this molecules. Does someone do it before? I know that FFGMX has one topology of FAD but are the parameters similar for FF53a61 in GMX 3.3.1? Thanks in advance. Samu

[gmx-users] Topolgy file FAD and ADP!

Dear Gmxers, i've trying to develop the topology files for FAD and ADP since the GMX 3.31 odes not have this molecules. Does someone it before? I know that FFGMX has one topology of FAD but are the parameters similar for FF53a61 in GMX 3.3.1? Thanks in advance. Samuel Pita. "Do not wear yourself

[gmx-users] Toplogy file FAD and ADP!

Dear Gmxers, i've trying to develop the topology files for FAD and ADP since the GMX 3.3.1 does not have this molecules. Does someone do it before? I know that FFGMX has one topology of FAD but are the parameters similar for FF53a61 in GMX 3.3.1? Thanks in advance. Samuel Pita. "Do not wear your

[gmx-users] re. missing atoms

Message: 2 Date: Tue, 01 Aug 2006 16:06:17 +0200 From: David van der Spoel <[EMAIL PROTECTED]> Subject: Re: [gmx-users] missing atoms Hi Ninoo, GROMACS will definitely give you warnings over missing atoms, but won't to the best of my knowledge replace them as David pointed out. Try downloading swi

Re: [gmx-users] problem using pairtypes 2, 3 for free-energy decoupling

Dear David, all, I'm not 100% sure that i'm doing everything right, mainly because I have found only a slight record about pairtypes 2,3 in the manual. And on the revision list for GROMACS 3.3 this feature is the very last on the list. So I wonder if it was really implemented in 3.3.1 release? Ho

Re: [gmx-users] Deshuffling atoms vs. residues

On Tuesday 01 August 2006 10:08, David van der Spoel wrote: > Jerome Henin wrote: > > Okay, now I have a partial answer to my own question. Apparently, when > > using the -sort and -shuffle options, the indexfile written by grompp > > undoes the shuffling, but not the sorting, so to speak. This bec

[gmx-users] Error on Deform

Hi, GMX-users, I encountered a problem when i sheared a cubic box of liquid using "deform" option. I set the option like this, "deform = 0 0 0 0 0.0005 0", but mdrun did not work. Add the output error is: --- Program mdrun, VERSION 3.3 Sourc

Re: [gmx-users] Failed to allocated u bytes of aligned memory (mdrun)

PAUL NEWMAN wrote: > PAUL NEWMAN wrote: > > Dear all: > > I made a simulation about a polyelectrolyte with some ions, it runs ok > > when I use cut-off for both Wdv and Coulomb. However I get the following > > error when I change it to PME. I attache my mdp file . Could someone > > help me to

Re: [gmx-users] Failed to allocated u bytes of aligned memory (mdrun)

Hi, Thanks Carsten for replying so fast. In my simulation I consider a single polyelectrolyte chain consisting of 50 charged beads of valency -1 with 50 oppositely charged counterions of same valency so my system is 100 atoms. My box simulation is 400 nm x 400 nm x 400 nm and the poly

Re: [gmx-users] PME usage in 3.3 & g_energy: doubt ?

Luca Mollica wrote: First, with rlist = rvdw, you will not get long range Lennard Jones interactions. In fact I would recommend using a larger vdw cut-off, as 0.9 is very short. Are you sure you are using the same mdp file? Yes it is and I have used the standard values suggested by GROM

Re: [gmx-users] PME usage in 3.3 & g_energy: doubt ?

First, with rlist = rvdw, you will not get long range Lennard Jones interactions. In fact I would recommend using a larger vdw cut-off, as 0.9 is very short. Are you sure you are using the same mdp file? Yes it is and I have used the standard values suggested by GROMACS guide. (3.2 and 3.

Re: [gmx-users] Failed to allocated u bytes of aligned memory (mdrun)

By the way, line 75 in fftgrid.c should read: gmx_fatal(FARGS,"Failed to allocate %u bytes of aligned memory.",size+32); (removed d in 'allocated' and fixed %u format specifier) Best, Jerome On Tuesday 01 August 2006 11:10, PAUL NEWMAN wrote: > PAUL NEWMAN wrote: > > Dear all: > > I made a simul

Re: [gmx-users] problem using pairtypes 2, 3 for free-energy decoupling

Alexey, I notice you haven't received a response on this; if you are convinced you're doing the right thing, you might try submitting a bugzilla so the developers can reproduce your problem. Thanks, David On 7/31/06, Alexey Shaytan <[EMAIL PROTECTED]> wrote: Dear Michael, Berk, all I'm curre

Re: [gmx-users] Failed to allocated u bytes of aligned memory (mdrun)

PAUL NEWMAN wrote: > Dear all: > I made a simulation about a polyelectrolyte with some ions, it runs ok > when I use cut-off for both Wdv and Coulomb. However I get the following > error when I change it to PME. I attache my mdp file . Could someone > help me to find what it's wrong in my file?. Th

Re: [gmx-users] PME usage in 3.3 & g_energy: doubt ?

First, with rlist = rvdw, you will not get long range Lennard Jones interactions. In fact I would recommend using a larger vdw cut-off, as 0.9 is very short. Are you sure you are using the same mdp file? About the LR coulomb, it will only appear if you have rlist < rcoulomb. In that case the s

[gmx-users] PME usage in 3.3 & g_energy: doubt ?

Hi, having started to use GMX 3.3 since few months, I have a doubt about using PME treatement for electrostatics and extracting energies from the corresponding .edr file. After simulation, trying to use g_energy -f energy.edr -o Energy.xvg, I get the following groups: [...] Mu-Y

[gmx-users] mmff94 with gmx

dear all// is there someone using the merck molecular force field (MMFF94) with gromacs? i am very interested in the parameters ... cheers// carsten -- dr carsten baldauf biotechnologisches zentrum der tu dresden http://www.biotec.tu-dresden.de/pisabarro http://www.biotec.tu-dresden.de/~carst

Re: [gmx-users] parallel in duals?

Jones de Andrade wrote: Ok, I know this subject have been discussed in the past. But I started to wander if the basic conclusion (do not use in parallel, you should rather use on job for each core) is still up, and if it is, if there is any hope of change in a foresight future, as well on how

Re: [gmx-users] missing atoms

ninoo mani wrote: Dear gmx users I have a protein molecule with few missing residues, a Lys with CG, CD, CE, NZ missing atoms, and a Val with CG1, CG2 missing atoms. I noticed that pdb2gmx reads the pdb file and places the missing atoms. Are you sure? I'm not aware of such a feature. First

Re: [gmx-users] Disulphide bonds

Cesar Araujo wrote: Cesar Araujo wrote: Hi, Anybody knows if there is some way to tell pdb2gmx to recognize automatically S-S bonds and not through the modification of specbond.dat file and -ss option??? it does if they are within the normal distance. are your pdb files ok? I want to force

Re: [gmx-users] Deshuffling atoms vs. residues

Jerome Henin wrote: Okay, now I have a partial answer to my own question. Apparently, when using the -sort and -shuffle options, the indexfile written by grompp undoes the shuffling, but not the sorting, so to speak. This became clear when I noticed that using just -shuffle without -sort produc

Re: [gmx-users] g_dipoles and fluctuation of the total dipole moment

Guido Humpert wrote: Hello, I want to use g_dipoles to calculate the dielectric constant epsilon of peptides. The peptides contain between 20 and 40 Aminoacids and are solvated in dodecahedron water box. How can I define the -mu option in a system with a water solvated peptid? your problem is

Re: [gmx-users] Failed to allocated u bytes of aligned memory (mdrun)

PAUL NEWMAN wrote: > Dear all: > I made a simulation about a polyelectrolyte with some ions, it runs ok > when I use cut-off for both Wdv and Coulomb. However I get the following > error when I change it to PME. I attache my mdp file . Could someone > help me to find what it's wrong in my file?.

[gmx-users] Disulphide bonds

Cesar Araujo wrote: Hi, Anybody knows if there is some way to tell pdb2gmx to recognize automatically S-S bonds and not through the modification of specbond.dat file and -ss option??? it does if they are within the normal distance. are your pdb files ok? I want to force some disulphide bond a

[gmx-users] Failed to allocated u bytes of aligned memory (mdrun)

Dear all: I made a simulation about a polyelectrolyte with some ions, it runs ok when I use cut-off for both Wdv and Coulomb. However I get the following error when I change it to PME. I attache my mdp file . Could someone help me to find what it's wrong in my file?. Thanks in advance.

Re: [gmx-users] g_dipoles and fluctuation of the total dipole moment

On Tue, 2006-08-01 at 12:39 +0200, Guido Humpert wrote: > Hello, > > I want to use g_dipoles to calculate the dielectric constant epsilon of > peptides. The peptides contain between 20 and 40 Aminoacids and are > solvated in dodecahedron water box. > How can I define the -mu option in a system wit

[gmx-users] g_dipoles and fluctuation of the total dipole moment

Hello, I want to use g_dipoles to calculate the dielectric constant epsilon of peptides. The peptides contain between 20 and 40 Aminoacids and are solvated in dodecahedron water box. How can I define the -mu option in a system with a water solvated peptid? How is the total dipole moment calculated

Re: [gmx-users] langevin dynamics

The bd_fric=0 results in the usage of mass/tau_t as the friction coefficient. You should find the tau_t option somewhere in the output as well. As David mentioned, changing tau_t changes the results. And this leads me to one question, as I see an increase in average temperature upon decreasin

Re: [gmx-users] langevin dynamics

On 7/31/06, [EMAIL PROTECTED] <[EMAIL PROTECTED] > wrote:Send gmx-users mailing list submissions toDate: Mon, 31 Jul 2006 07:21:46 -0700 From: "David Mobley" <[EMAIL PROTECTED]>Subject: Re: [gmx-users] langevin dynamicsGerrit is right, with "sd", the friction is set by tau_t, as described in the se