Re: [gmx-users] How to remove H atom from residue in gro file?

Hi Maik, Thanks for the warning and the tip, I have already donwloaded and will read that paper today, it seems to be what I need. I have been working with MD for some 6 months now (I know that's not much), and have had the help of some knowledgeable people, but they are unavailable right now. I

[gmx-users] problem regarding grompp

Hi all, I have been trying to simulate peptide (octa alanine). In genbox i have inserted 40 molecule of guanidium ion 800 water molecule (by -ci maxsol option in gromacs 3.3.3)then again with genbox i added 40 molecules of thiocynate ion 80 water molecules as above mentioned way. When i tried

[gmx-users] GMX CPMD K+ ion problem

Dear all, We successfully passed all examples in GMX-CPMD and some other stuff with amberff with common atoms, but since we trying to deal with K+ (potassium) in QM part, we see every time absence of potassium in CPMD_inp.run, it's just skipped. In very beginning CPMD shows right number of atoms

Re: [gmx-users] error while running grompp

Ragothaman Yennamalli wrote: Dear all, We are trying running Gromacs in different systems with different number of processors. In sun opteron cluster we checked and it ran perectly fine. When, using the same input files, to run in apple g5 system with same number of processors. I get the

Re: [gmx-users] problem regarding grompp

[EMAIL PROTECTED] wrote: Hi all, I have been trying to simulate peptide (octa alanine). In genbox i have inserted 40 molecule of guanidium ion 800 water molecule (by -ci maxsol option in gromacs 3.3.3)then again with genbox i added 40 molecules of thiocynate ion 80 water molecules as above

Re: [gmx-users] GMX CPMD K+ ion problem

For the Gromacs-CPMD interface you have to specify the QM groups in your .mdp file like this QMMM-grps= QM_part. Then open your index file and create an atom group with the same name QM_part and add in it all atoms that you want to treat with CPMD. If this doesn't work you should

[gmx-users] Virtual site and constraints

Hello! I would like to involve formate molecule (HCOO-)in my dynamics, but I have the problem when I use virtual site (type 3fd)for it. When I run grompp for single formate molecule, it`s ok. But after solvating in bath of solvent (tip3p) grompp runs with error: Cleaning up constraints and

Re: [gmx-users] How to remove H atom from residue in gro file?

Dear All, In working with Nelson on his problem (below), I made some headway into figuring out what is going on with the ffG43a1p force field files. I know a few others have asked questions about it across this list, so I thought I would send this out to everyone. By modifying a few entries in

Re: [gmx-users] FEP trajectory errors

Thank you David and Maik for your detailed replies. Yes, I am trying to obtain an absolute free energy of binding. My thermodynamic cycle is: NT+DNA(adsorbed) - NT+ DNA(desorbed) (obviously this is not the one that I'm obtaining with the alchemic method) Thus, the one I'm using in the

[gmx-users] Gromacs installation: cannot find LibXmu.la

On SuseLinux 10.3 the command ./configure --enable-mpi works fine but make terminates at this point. Using the option --disable-shared did not change anything. I would be grateful for any help. Many thanks Andreas Output of make: mv -f .deps/nb_free_energy.Tpo .deps/nb_free_energy.Plo

Re: [gmx-users] Gromacs installation: cannot find LibXmu.la

Hi Andreas, try ./configure --enable-mpi --without-x Carsten Am 18.01.2008 um 09:45 schrieb Andreas Kukol: On SuseLinux 10.3 the command ./configure --enable-mpi works fine but make terminates at this point. Using the option --disable- shared did not change anything. I would be

[gmx-users] Virtual site and constraints

Hello! I would like to involve formate molecule (HCOO-)in my dynamics, but I have the problem when I use virtual site (type 3fd)for it. When I run grompp for single formate molecule, it`s ok. But after solvating in bath of solvent (tip3p) grompp runs with error: Cleaning up constraints and

Re: [gmx-users] Gromacs installation: cannot find LibXmu.la

I think I saw this before... check if openmotif contains this library and install it or just try. ./configure --without-x --enable-mpi Cheers, Diego Enry. On Jan 18, 2008 6:45 AM, Andreas Kukol [EMAIL PROTECTED] wrote: On SuseLinux 10.3 the command ./configure --enable-mpi works fine but make