[gmx-users] Error in .top when running grompp for final product MD

Dear gromacs users, I am running MD for a protein with 212 amino acid residues. When I run grompp (grompp -f pn_md.mdp -c pn_md.pdb -r pn_md.pdb -p pn.top - o pn_md.tpr ) for the final product MD, I receive the following error message. I properly included sol and ion in the temperature contro

[gmx-users] Interaction energy calculation in a radius

Hi all, I want to calculate interaction energy between my ligand and residues of proetins which come within 6A of any atoms of the raidus. I have defined those residues and ligand as different groups. But how to select water around 6A radius of the ligand during dynamicsfor the calculation. If I co

[gmx-users] dihedral

Dear Gromacs users, Thanks a lot for your input so far. my problem regarding the dihedral angle still suffering me. I need to rotate a bond by certain angle, say from 30 to 150 degrees. i would like to see how the peptide will change its conformation for example CIS to TRANS by the rotation. I tri

Re: [gmx-users] Are the constraint forces included intheforcesoutputed in the

Could you please tell me if the constraint forces are included in the forces outputed in the trr file? Constraint forces are not included. We should state this somewhere in the manual. I wondered about this before as well. Shouldn't we include them anyway? It is quite important when you us

[gmx-users] gromacs 4 release date?

Any projection date for a release? Of particular interest to me is whether it is very likely to come out before Jan 1 2008. I have heard that v4 is expected to scale better for parallel runs than previous versions, is this correct? If so, how close to the namd scaling might gromacs get?

Re: [gmx-users] tau_p

> Hi, > > Well, tau_p rather controls how the pressure fluctuates around the > average..., ref_p is your attempt to control the average (if your > system is set up properly). Yeah, that :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http:

Re: [gmx-users] problem with genion

No, i am not. you? On a serious note, bug 108 that David referred to (last modified this morning) suggests compilaton problems with gcc4 due to pbc.c, which doesnt sound healthy. The same bugzilla page has a possible cure with suggestion to use gcc3, but changing from one gcc to another is not

Re: [gmx-users] tau_p

Hi, Well, tau_p rather controls how the pressure fluctuates around the average..., ref_p is your attempt to control the average (if your system is set up properly). Cheers, Tsjerk On 1/5/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > Dear all, > I am running md simulations on a decapeptide, us

Re: [gmx-users] About g_cluster

Brigo et al. Biophys J. (2005) 88:3072 Smith et al. Proteins (2002) 48:487 Ciao Caterina Cesar Araujo ha scritto: Hi, Can anybody give some reference about a good explanation on how to use g_cluster in order to analyze a set of simulations on complexes differing one each other in their start

Re: [gmx-users] problem with genion

> While using genion with -np 3, i get 2 lines of Replacing sol. xxx with Na > and it hangs up. With -np 1 it works fine and replaces 1 SOL with Na. I > thought it might be my system, so went to /tutor/speptide, but it was the > same behaviour. I am using gromacs 3.3.1. As I recall genion worked fi

Re: [gmx-users] afm does not work!

> hi everyone > I need to pull the two parallel monolayers together,the two monolayers > are in the x-y plane , so i pull the one along the z direction,but it > stay still! i tried several times ,but all failed! > i use the > [position_restraints ] > 1 1 9 9 4000 > 2 1

Re: [gmx-users] tau_p

> Dear all, > I am running md simulations on a decapeptide, using pressure coupling > [npt]. > My box is octahedral and box dimensions are set at peptide length plus > twice > the cut-off as recommended. I have set tau_p to be 1.0 ps. After 1 ns , > the > average pressure had come down to 2.6 bar,

Re: Re: Re: [gmx-users] Installation of Gromacs and speed...

> Thank you for the reply. I have some more queries: > So if I load Gromacs 3.3.1 on Octane will I gain on the time a bit ? Maybe... depends if there were any meaningful speed-ups in parts of the code you actually use. > Do you suggest me to update the Gromacs versions on both the systems to > Gr

Re: [gmx-users] problem with genion

Abil Aliev wrote: While using genion with -np 3, i get 2 lines of Replacing sol. xxx with Na and it hangs up. With -np 1 it works fine and replaces 1 SOL with Na. I thought it might be my system, so went to /tutor/speptide, but it was the same behaviour. I am using gromacs 3.3.1. As I recall ge

Re: [gmx-users] problem regarding xmgr

sangeeta wrote: Dear GROMACS list members, It may be a very trivial question,But I can not solve it, please help,The commands like xmgrace,xpsview,xmgr, my-dssp are not working. How could I get out of that problem? regards Sangeeta -- Open WebMail Project (http://openwebmail.org) ___

[gmx-users] problem regarding xmgr

Dear GROMACS list members, It may be a very trivial question,But I can not solve it, please help,The commands like xmgrace,xpsview,xmgr, my-dssp are not working. How could I get out of that problem? regards Sangeeta -- Open WebMail Project (http://openwebmail.org) ___

[gmx-users] tau_p

Dear all, I am running md simulations on a decapeptide, using pressure coupling [npt]. My box is octahedral and box dimensions are set at peptide length plus twice the cut-off as recommended. I have set tau_p to be 1.0 ps. After 1 ns , the average pressure had come down to 2.6 bar, though fluctuat

[gmx-users] problem with genion

While using genion with -np 3, i get 2 lines of Replacing sol. xxx with Na and it hangs up. With -np 1 it works fine and replaces 1 SOL with Na. I thought it might be my system, so went to /tutor/speptide, but it was the same behaviour. I am using gromacs 3.3.1. As I recall genion worked fine un

[gmx-users] afm does not work!

hi everyone I need to pull the two parallel monolayers together,the two monolayers are in the x-y plane , so i pull the one along the z direction,but it stay still! i tried several times ,but all failed! i use the [position_restraints ] 　　 1 1 9000

Re: [gmx-users] Installation of Gromacs and speed...

Swamy Kakumani, Thank you for the reply. I am not working on the parallel machines, Linux version is Fedora Core 4 System's configuration is listed below in my previous mail. regards sharada -- Original Message -- From: swamy kakumani <[EMAIL PROTECTED]> To: [EMAI

Re: [gmx-users] Are the constraint forces included inthe forcesoutputed in the

From: David van der Spoel <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] Are the constraint forces included inthe forcesoutputed in the Date: Fri, 05 Jan 2007 10:40:18 +0100 Berk Hess wrote: From: "Pu Liu

Re: [gmx-users] Are the constraint forces included in the forcesoutputed in the

Berk Hess wrote: From: "Pu Liu" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] Are the constraint forces included in the forcesoutputed in the trr file? Date: Fri, 05 Jan 2007 00:34:03 + Dear GROMACS list members, Coul

RE: [gmx-users] Are the constraint forces included in the forcesoutputed in the

From: "Pu Liu" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] Are the constraint forces included in the forcesoutputed in the trr file? Date: Fri, 05 Jan 2007 00:34:03 + Dear GROMACS list members, Could you please tell