Re: [gmx-users] 4.0_beta1: 1 particles communicated to PME node 9 are more than a cell length out of the domain decomposition cell of their charge group

andrea spitaleri wrote: Hi again, in addition to the previous post, 4.0_beta1 crashes using 27 cpus and option -dd 3 3 3, whereas it goes fine using 24 cpus and not -dd option. any clue? Regards, andrea Maybe you can upload a bugzilla with exact command line and tpr file. -- David van der

Re: [gmx-users] D2O

Quote: "*A D2O gromacs mailing lists query will produce (among others) the following results which might be of assistance to you:* " I would like to know how do such a query. I think that under the web interface one can access archive per date, w/out searching. --Omer Markovitch.

Re: [gmx-users] OPLS force field does not recognize Atom type

Morteza Khabiri wrote: Dear As you said I change the name of the itp file to opls_xxx. It works. thank you very much. But now i faced with new problem. I got new error: Fatal error: Incorrect number of parameters - found 4, expected 6 or 12. It was probably printed with a line number in th

Re: [gmx-users] D2O

Hi Chih-Ying Lin, besides supporting Christophers general comments, I would just add that there actually are D2O models available in literature: An effective pair potential for heavy water J.Chem.Phys. (2001) v. 114, Issue 18, pp. 8064-8067. I would also like to point you in the direction of

[gmx-users] OPLS force field does not recognize Atom type

Dear As you said I change the name of the itp file to opls_xxx. It works. thank you very much. But now i faced with new problem. I got new error: Fatal error: Incorrect number of parameters - found 4, expected 6 or 12. what does it mean? Thank you in advance Morteza __

Re: [gmx-users] D2O

Well, from a simulation standpoint these systems are usually regarded as having identical structures at a classical level; the dynamics are a bit slower due to the heavier D vs. H, but this does not affect the solution structure. The force fields are identical except for the heavier mass.

[gmx-users] D2O

Hi I would like to simulate the solutes are embeded in D2O solution. Could someone explain the difference of simulating D2O solution and H2O solution? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/list

Re: [gmx-users] fatal errors regarding grid cells

NAMD GROMACS wrote: Hi, I am getting this error number of times when I am trying to run Md with a 9 residue peptide in water box using spc216.gro It says "Number of grid cells is zero. Probably the system and box collapsed." earlier after grompp it gives me warning that the protein atom n

[gmx-users] fatal errors regarding grid cells

Hi, I am getting this error number of times when I am trying to run Md with a 9 residue peptide in water box using spc216.gro It says "Number of grid cells is zero. Probably the system and box collapsed." earlier after grompp it gives me warning that the protein atom number is less than 10% of t

Re: [gmx-users] OPLS force field does not recognize Atom type

* Morteza Khabiri <[EMAIL PROTECTED]> [2008-09-09 22:03:36 +0200]: Dear I want to make the solution which is not working with unified atom force fields. Then I decided to make the itp file by my own. I made the all atom type itp file for opls AA. I found all of the opls feature in gromacs to

Re: [gmx-users] OPLS force field does not recognize Atom type

Morteza Khabiri wrote: Dear I want to make the solution which is not working with unified atom force fields. Then I decided to make the itp file by my own. I made the all atom type itp file for opls AA. I found all of the opls feature in gromacs top directory and according to the top direct

[gmx-users] OPLS force field does not recognize Atom type

Dear I want to make the solution which is not working with unified atom force fields. Then I decided to make the itp file by my own. I made the all atom type itp file for opls AA. I found all of the opls feature in gromacs top directory and according to the top directory files I made the new it

Re: [gmx-users] still some problems with HP-UX... grompp acting weird

On Sep 9, 2008, at 3:31 PM, David van der Spoel wrote: Christopher Daub wrote: On Sep 9, 2008, at 12:43 PM, David van der Spoel wrote: Christopher Daub wrote: On Sep 9, 2008, at 2:53 AM, David van der Spoel wrote: Christopher Daub wrote: Hey again! The install of gromacs 3.3.3 on HP-UX is

[gmx-users] trjconv

Dear Users, I have a question about the option -fit in trjconv. The default option with -fit is none. If I use the option as rot+trans, does it mean that the rotational and translational motions are removed from the trajectory ? If not, is there any option in gromacs, to create a translational an

Re: [gmx-users] still some problems with HP-UX... grompp acting weird

Christopher Daub wrote: On Sep 9, 2008, at 12:43 PM, David van der Spoel wrote: Christopher Daub wrote: On Sep 9, 2008, at 2:53 AM, David van der Spoel wrote: Christopher Daub wrote: Hey again! The install of gromacs 3.3.3 on HP-UX is mostly working fine, but I'm getting some weird behavio

Re: [gmx-users] still some problems with HP-UX... grompp acting weird

On Sep 9, 2008, at 12:43 PM, David van der Spoel wrote: Christopher Daub wrote: On Sep 9, 2008, at 2:53 AM, David van der Spoel wrote: Christopher Daub wrote: Hey again! The install of gromacs 3.3.3 on HP-UX is mostly working fine, but I'm getting some weird behaviour from grompp where it

Re: [gmx-users] D2O

Chih-Ying Lin wrote: Hi Does Gromacs support D2O simulation? Is it any difference between the D2O and H2O except the molecular weight? and, how about the force field parameters? are the two systems just the same? If you have a flexible model you would have to change the force constants, for a

[gmx-users] D2O

Hi Does Gromacs support D2O simulation? Is it any difference between the D2O and H2O except the molecular weight? and, how about the force field parameters? are the two systems just the same? Thank you Lin ___ gmx-users mailing listgmx-users@groma

[gmx-users] I invite you to see MyDailyFlog page!

Hi! I would like to invite you to visit MyDailyFlog and see my latest photos. Check out: http://www.mydailyflog.com/sunitabioinfo Cheers! sunita gupta Got a digital camera? MyDailyFlog is a personal photo-blogging space where you can easily post your

Re: [gmx-users] still some problems with HP-UX... grompp acting weird

Christopher Daub wrote: On Sep 9, 2008, at 2:53 AM, David van der Spoel wrote: Christopher Daub wrote: Hey again! The install of gromacs 3.3.3 on HP-UX is mostly working fine, but I'm getting some weird behaviour from grompp where it doesn't set the output filename correctly. Here is the g

Re: [gmx-users] still some problems with HP-UX... grompp acting weird

On Sep 9, 2008, at 2:53 AM, David van der Spoel wrote: Christopher Daub wrote: Hey again! The install of gromacs 3.3.3 on HP-UX is mostly working fine, but I'm getting some weird behaviour from grompp where it doesn't set the output filename correctly. Here is the grompp output from whe

[gmx-users] genion problem with large systems

Hi all, I'm experiencing a strange problem with genion that I have never seen before. I am preparing some membrane systems, many of which involve a large number of charged lipids (several hundred). When using lipids with PC headgroups (no net charge), the following works fine: genion -s i

[gmx-users] 4.0_beta1: 1 particles communicated to PME node 9 are more than a cell length out of the domain decomposition cell of their charge group

Hi again, in addition to the previous post, 4.0_beta1 crashes using 27 cpus and option -dd 3 3 3, whereas it goes fine using 24 cpus and not -dd option. any clue? Regards, andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute

[gmx-users] 4.0_beta1: 1 particles communicated to PME node 9 are more than a cell length out of the domain decomposition cell of their charge group

Hi there, my system is about 200,000 atoms. we have installed the latest version (4.0_beta1) on our cluster but i get the follow error after few calculation ps : 1 particles communicated to PME node 9 are more than a cell length out of the domain decomposition cell of their charge group simi

Re: [gmx-users] g_dist

minnale wrote: Hi all, I want to calculate distance of protein residues by using g_dist, now I have doubt that 1.Is it possible to calculate distance for more than two residues of two comparable systems? g_dist calculates a simple center-of-mass distance between two points. What kind o

[gmx-users] g_dist

Hi all, I want to calculate distance of protein residues by using g_dist, now I have doubt that 1.Is it possible to calculate distance for more than two residues of two comparable systems? 2. which type of group select for generating index file?_

Re: Re: [gmx-users] conversion?

thanks alot Justin for your reply On Tue, 09 Sep 2008 Justin A.Lemkul wrote : > > >minnale wrote: >> Hi all, >> I am interested about analyse some of the results with amber and gromacs >> md packages. Could anyone tell me how to convert .xtc of gromacs to >> trajectory input for amber. >>

Re: [gmx-users] conversion?

minnale wrote: Hi all, I am interested about analyse some of the results with amber and gromacs md packages. Could anyone tell me how to convert .xtc of gromacs to trajectory input for amber. eagerly waiting for reply The *exact* same question was asked yesterday: http://www.gromacs.o

Re: [gmx-users] Doubt in Energy minimization and Position restrained

vivek sharma wrote: Hi there, My apologies for asking question from basics. I have one doubt regarding order of Position restrained and Energy minimization. While running Position restrained, it soaks water molecule well within the protein molecule. In doing so on rearranging atoms it will

[gmx-users] Doubt in Energy minimization and Position restrained

Hi there, My apologies for asking question from basics. I have one doubt regarding order of Position restrained and Energy minimization. While running Position restrained, it soaks water molecule well within the protein molecule. In doing so on rearranging atoms it will again raise the energy of s