Re: [gmx-users] problems running grompp with protein-ligand complex

Hi Fabrício, > I've checked wikigromacs, but the solution given there, to simply erase the > second default line does not suit me here. Once I do this, i mean, go to my > ligand.itp file and put a ; before my default section, grompp does not > recognize anymore that my ligand is there and gives ou

Re: [gmx-users] no density option in g_energy

Dear Justin, Thankk you very much for yr reply. I have forgotten that my system is under NVT condition. Thanks. QIU YI HUAN DEPARTMENT OF CHEMISTRY, FACULTY OF SCIENCE, UNIVERSITY PUTRA MALAYSIA, MALAYSIA. --- On Thu, 11/27/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > From: Justin A. Le

[gmx-users] Re: Re: Loss of bonds in HEME iron after pdb2gmx

Hi Justin, Thanks a lot for the suggestions regarding the force field and the sulphide bond. The bond is now formed after changing the distance range in specbond.dat. Thanks. Sarada > > Message: 2 > Date: Wed, 26 Nov 2008 07:21:37 -0500 > From: "Justin A. Lemkul" <[EMAIL PROTECTED]> > Subject: Re:

[gmx-users] Re: About entropic contribution to the potential of mean force

I've got it! Thanks myself. ^_^ So, it seems that the prior calculations by, i.e. Ciccotti, et al, Chem. Phys. 129, 241 (1989), Guardia, et al, J. Chem. Phys. 95, 2823 (1991) are flawy since they have not corrected the entropic effects at all. Cheers, zgzhang > Date: Wed, 26 Nov 2008 15:55:05

Re: [gmx-users] SMP/Parallel mdrun

Ian Stokes-Rees wrote: Hi Mark, Mark Abraham wrote: Terminology - GROMACS is not threaded, but uses MPI processes for parallelism. Yes, I gathered that. I have an MPI-compiled version of gromacs v4.0 and am attempting to get parallel execution on a 2x2 core AMD Opteron system via: $ lamboo

Re: [gmx-users] SMP/Parallel mdrun

Hi Mark, Mark Abraham wrote: Terminology - GROMACS is not threaded, but uses MPI processes for parallelism. Yes, I gathered that. I have an MPI-compiled version of gromacs v4.0 and am attempting to get parallel execution on a 2x2 core AMD Opteron system via: $ lamboot $ mdrun -np 4 -s ../1W

Re: [gmx-users] SMP/Parallel mdrun

Ian Stokes-Rees wrote: I am a computational scientist working with a physical chemist to try to parallelize her use of gromacs -- today is my first day using the application and I am not succeeding in getting multiple threads. Terminology - GROMACS is not threaded, but uses MPI processes for

[gmx-users] SMP/Parallel mdrun

I am a computational scientist working with a physical chemist to try to parallelize her use of gromacs -- today is my first day using the application and I am not succeeding in getting multiple threads. I have an MPI-compiled version of gromacs v4.0 and am attempting to get parallel execution

Re: [gmx-users] no density option in g_energy

Q. Y. HUAN wrote: Dear all, Why there is no density option when I do g_energy amalyzation. This question was asked just a few weeks ago (hint: search the list for answers!). Searching "no density g_energy" will lead you to this: http://www.gromacs.org/pipermail/gmx-users/2008-November/

[gmx-users] no density option in g_energy

Dear all, Why there is no density option when I do g_energy amalyzation. thanks QIU YI HUAN DEPARTMENT OF CHEMISTRY, FACULTY OF SCIENCE, UNIVERSITY PUTRA MALAYSIA, MALAYSIA. ___ gmx-users mailing listgmx-users@gromacs.org http://www.grom

Re: [gmx-users] problems running grompp with protein-ligand complex

Can you post the contents of your ligand.itp? -Justin Ragnarok sdf wrote: I am working with a protein-ligand complex in gromacs with ffamber99 forcefield. I was able to generate the topology file for my ligand with acpypi. Was also able to insert the ligand coordinates into my protein's coord

[gmx-users] problems running grompp with protein-ligand complex

I am working with a protein-ligand complex in gromacs with ffamber99 forcefield. I was able to generate the topology file for my ligand with acpypi. Was also able to insert the ligand coordinates into my protein's coordinate file. Was also able to generate the water box with genbox. The number of m

Re: [gmx-users] Concentration

Chih-Ying Lin wrote: Hi How to make a solution with specific concentration ? Concentration of what? For ions, use genion -conc; for other solute molecules, do some simple stoichiometry from General Chemistry based on the box volume. Command 1 => editconf -d 0.75 -bt cubic 0.75=Dista

[gmx-users] Concentration

Hi How to make a solution with specific concentration ? Command 1 => editconf -d 0.75 -bt cubic 0.75=Distance between the solute and the box cubic = the type of the simulation box Command 2 => genbox -cp solute.gro -cs spc.gro -box Y Y Y Y = the box vector in nm If I use cubic in my system, i

Re: [gmx-users] genbox -ci solute.gro -nmol N

Chih-Ying Lin wrote: Hi Originally, in the topol.top file => [molecule] solute 1 After the command: genbox -cp one_solute.gro -cs spc216.gro -ci one_solute.gro -nmol N -p topol.top in the topol.top file => [molecule] solute 1 solvent 5000 I think the flag "-p topol.top" in the genb

[gmx-users] genbox -ci solute.gro -nmol N

Hi Originally, in the topol.top file => [molecule] solute 1 After the command: genbox -cp one_solute.gro -cs spc216.gro -ci one_solute.gro -nmol N -p topol.top in the topol.top file => [molecule] solute 1 solvent 5000 I think the flag "-p topol.top" in the genbox command did not do it corr

Re: [gmx-users] course grain model for DNA

He, Yang wrote: Hi Justin, Thank you for your reply. In fact , for this base pair of "Gb2 Cb2 1 0.000194e10 0.00217e4", whatever I do , the final result for this base pair is the same they will always separate from each other. Hence, I doubt whether this is because gromacs did

Re: [gmx-users] course grain model for DNA

He, Yang wrote: Hi Mrinalini. Thank you for your suggestions. In my previous case, I never use the distance restraints . So I wonder whether you can provide me a sample for file of the disres.itp .In fact, I don't know much about this file' form and how to set values in the file. Manual

RE: [gmx-users] course grain model for DNA

Hi Mrinalini. Thank you for your suggestions. In my previous case, I never use the distance restraints . So I wonder whether you can provide me a sample for file of the disres.itp .In fact, I don't know much about this file' form and how to set values in the file. Thank you. Yang

RE: [gmx-users] course grain model for DNA

Hi Justin, Thank you for your reply. In fact , for this base pair of "Gb2 Cb2 1 0.000194e10 0.00217e4", whatever I do , the final result for this base pair is the same they will always separate from each other. Hence, I doubt whether this is because gromacs did not read my force f

[gmx-users] Problems with distance restraints

It's not really a solution, but you could try a different number of nodes. I have found that even regular topologies might run on N nodes, but not N+A nodes, giving the error messaeg that you post below. Chris. -- original message -- Hi all, I am trying to use a simple scheme to restrain a

Re: [gmx-users] Bugs in gromacs 4

Jochen Hub wrote: Jelger Risselada wrote: Finally had a look through the gromacs 4.0 source code. Don't know if this bug/points already have been reported and changed in 4.0.2: 1) There is never memory allocated for the pointers to the user defined groups: mdatoms->cU1 etc. I'm not s

Re: [gmx-users] Bugs in gromacs 4

Jelger Risselada wrote: > Finally had a look through the gromacs 4.0 source code. > Don't know if this bug/points already have been reported and changed in > 4.0.2: > > 1) There is never memory allocated for the pointers to the user defined > groups: > > mdatoms->cU1 etc. I'm not sure, but there

Re: [gmx-users] Re: how to show dodecahedron box in VMD

Thanks lot. Happy Thanksgiving!. -Xianghong Qi On Wed, Nov 26, 2008 at 8:53 AM, Alessandro Casoni < [EMAIL PROTECTED]> wrote: > Tsjerk Wassenaar ha scritto: > >> Hi, >> >> Can't help you with VMD, but I do have a script to take care of this in >> Pymol. >> >> Cheers, >> >> Tsjerk >> >> On 11/25/0

[gmx-users] Bugs in gromacs 4

Finally had a look through the gromacs 4.0 source code. Don't know if this bug/points already have been reported and changed in 4.0.2: 1) There is never memory allocated for the pointers to the user defined groups: mdatoms->cU1 etc. These pointers will stay NULL when a user defined group is

[gmx-users] gmx-users@gromacs.org

Finally had a look through the gromacs 4.0 source code. Don't know if this bug/points already have been reported and changed in 4.0.2: 1) There is never memory allocated for the pointers to the user defined groups: mdatoms->cU1 etc. These pointers will stay NULL when a user defined group i

Re: [gmx-users] Problems with distance restraints

Please disregard my message. I had a typo in my atom numbers that I was restraining. Apparently the distance between atoms 1016 and 559 is far greater than 0.376 nm, thus generating the error. -Justin Justin A. Lemkul wrote: Hi all, I am trying to use a simple scheme to restrain a few dis

[gmx-users] Problems with distance restraints

Hi all, I am trying to use a simple scheme to restrain a few distances within my protein, which is contained within an octahedral box of SPC water. In place of distance restraints, I'm using bond type 6 to utilize a harmonic potential to restrain the distance between a few atoms. When I imp

Re: [gmx-users] Re: how to show dodecahedron box in VMD

Tsjerk Wassenaar ha scritto: Hi, Can't help you with VMD, but I do have a script to take care of this in Pymol. Cheers, Tsjerk On 11/25/08, xianghong qi <[EMAIL PROTECTED]> wrote: Dear all: I am trying to show the dodecahedron box only in vmd since my simulation box is dodecahedron. If

Re: [gmx-users] Re: Loss of bonds in HEME iron after pdb2gmx

Justin A. Lemkul wrote: S and Fe atoms to be 0.25 +/- 0.2 nm apart. If they are much further Edit that: 0.25 nm +/- 0.02 nm. Apparently my math (and/or typing) skills are suspect first thing in the morning :) -Justin -- Justin A. Lemkul Graduat

Re: [gmx-users] Re: Loss of bonds in HEME iron after pdb2gmx

[EMAIL PROTECTED] wrote: Hi Justin, Thanks for your reply. I am using the gmx Gromacs Forcefield. As you said the topology file does contain the bonds and I need not have made the modificatins to specbond.dat. But using the original specbond.dat does not prevent the protonation of CYS. I rename

RE: [gmx-users] List of all bonds form tpr file?

I just realized that in 4.0 I modified things such that it only prints the bonds per molecule type. It would be quite easy to modify a program to write all bonds. (mk_angdx for instance). If you just have one atom type you can easily modify your script by reading the number of molecules and atoms

Re: [gmx-users] correct processing of #define statements by grompp in gromacs 4.0.2 requires exactly one space after #define

Hi, I also encoutered a strange behaviour of gmxcpp when using B-states. When I set up up a free energy simulation (gromacs 4.0.2) with amber03 (ffamber from Sorin & Pande), I define a dihedral angle, e.g. like [ dihedrals ] . 511 515 517 513 3 aromatic_prop_5aaromatic_prop_5 . I

RE: [gmx-users] List of all bonds form tpr file?

Hi, gmxdump in 4.0 still dumps all bonds. I don't know what causes you not to see them. Berk > Date: Wed, 26 Nov 2008 02:09:08 -0800 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gmx-users] List of all bonds form tpr file? > > Dear All, > We have a script, which visualizes

RE: [gmx-users] Using double precision files with single precision version

Hi, This works fine. All Gromacs file format/programs are single/double compatible both ways. Reading a double precision file with a single precision program, or course, gives single precision results. But there is probably no property that is significantly affected by this. Berk > Date: Wed, 2

Re: [gmx-users] Re: how to show dodecahedron box in VMD

Hi, Can't help you with VMD, but I do have a script to take care of this in Pymol. Cheers, Tsjerk On 11/25/08, xianghong qi <[EMAIL PROTECTED]> wrote: > Dear all: > > I am trying to show the dodecahedron box only in vmd since my simulation box > is dodecahedron. If I include water, I can see t

[gmx-users] List of all bonds form tpr file?

Dear All, We have a script, which visualizes the bonds in the coarse-grained system simulated in gromacs. In gromacs 3.x it was reading dumps of the tpr files and extracted BONDS records. Now in 4.x it does not work because gmxdump no longer outputs all bonds in the system. Is it possible to ext

Re: [gmx-users] Analyzing a trajectory split over multiple files

On Tue, Nov 25, 2008 at 01:47, Suman Chakrabarty <[EMAIL PROTECTED]>wrote: > Dear all, > > I have a very long trajectory split over a large number of files. What > would be the most efficient way to use the analysis programs over them? > Do they support multiple input for trajectory? Or I need to

Re: [gmx-users] Replacing molecules in .gro coordinate file

> > > Supposed I have a .gro file of 38 molecules of A which are already in > equilibrated conformations. Now I want to transform 15 molecules of A into B > therefore I will have the binary mixture of A/B with 13:15 molar ratio in > the final structure. How can I do this? Any suggestions will be ap

Re: [gmx-users] Using double precision files with single precision version

vivek sharma wrote: Hi All, I had a few MD runs with double precision in gromacs, Can I use single precision version of gromacs to play with those files e.g making movie files and extracting h_bond information. I am afraid if it will affect my results. I don't know whether it does work, but

[gmx-users] About entropic contribution to the potential of mean force

Hi, In the manual of gromacs, the entropic contribution to the pmf is emphasized. In my opinion, this contribution is originated from the rotations of the constrained groups. However, according to the manual suggestion, "...when calculating a PMF between two solutes in a solvent, for the pu