Re: [gmx-users] How could I know whether I should use epsilon-sigma or c6-c12?

2012-06-04 Thread Mark Abraham
On 5/06/2012 4:34 PM, Bao Kai wrote: Hi, all, I am still trying to do my simulation with liquid mixtures. I have a simple question now. When I writing my .top file, how could I know if I should use epsilon-sigma or c6-c12 parameters for the LJ potential? It seems that in some examples, c6-c12 p

[gmx-users] Dielectric Constants

2012-06-04 Thread Size Zheng
Dear All, I would like to calculate the dielectric constant of an ice crystal system in a simulation had about 1 ms. I used g_dipoles command to do this. The obtained results seemed that they were only the values of the last frame in the simulation but not the average values, Dipole moment (De

[gmx-users] How could I know whether I should use epsilon-sigma or c6-c12?

2012-06-04 Thread Bao Kai
Hi, all, I am still trying to do my simulation with liquid mixtures. I have a simple question now. When I writing my .top file, how could I know if I should use epsilon-sigma or c6-c12 parameters for the LJ potential? It seems that in some examples, c6-c12 parameters are used and epsilon-sigma pa

[gmx-users] selenomethionine OPLS ff

2012-06-04 Thread tarak karmakar
Dear Gromacs Users, While dealing with a protein I am facing problem with the selenomethionins (MSE) residue. I couldn't find the parameters for that residue. So can anyone suggest me any literature where I can find the OPLS force-filed parameters for the same ? Thanks Regards T

Re: [gmx-users] Writing and compiling new analyses for gromacs

2012-06-04 Thread Mark Abraham
On 5/06/2012 9:11 AM, Peter C. Lai wrote: The quick and dirty way is to post-patch Makefile in src/tools. I think patching the appropriate Makefile.in is sufficient for configure to pick up and automake into Makefile if all you need to do is append a make target. As to your previous question, o

Re: [gmx-users] Writing and compiling new analyses for gromacs

2012-06-04 Thread Peter C. Lai
The quick and dirty way is to post-patch Makefile in src/tools. I think patching the appropriate Makefile.in is sufficient for configure to pick up and automake into Makefile if all you need to do is append a make target. As to your previous question, on our cluster, I use Intel ICC 11.1.056 bo

Re: [gmx-users] Writing and compiling new analyses for gromacs

2012-06-04 Thread Shay Teaching
One more question: How do I get my new g_whatever analysis to be included in the compilation? Simply placing my file in src/tools won't work of course. How to I place it correctly in the build? Thanks, -Shay 2012/6/5 Justin A. Lemkul > > > On 6/4/12 5:16 PM, Shay Teaching wrote: > >> >> >> 2012/

Re: [gmx-users] Writing and compiling new analyses for gromacs

2012-06-04 Thread Shay Teaching
2012/6/5 Justin A. Lemkul > > > On 6/4/12 5:16 PM, Shay Teaching wrote: > >> >> >> 2012/6/4 Justin A. Lemkul mailto:jalem...@vt.edu>> >> >> >> >> >>On 6/4/12 2:59 PM, Shay Teaching wrote: >> >>Dear Gromacs users, >> >>I want to write new analyses for gromacs and compile it (so

[gmx-users] Angle deformation of Triphosphate moiety with charge -4 ?..

2012-06-04 Thread Alberto Sergio Garay
Hi all I'm trying to simulate a UTP (Uridin Tryphosphate) with charge -4: O(-) O(-) O(-) | | | --O--P--O--P--O--P--O(-) | | | O O O I've used the triphosphate charge parameters published by Oliveira et al(1). They used the RESP procedure after ca

Re: [gmx-users] Writing and compiling new analyses for gromacs

2012-06-04 Thread francesco oteri
Dear Peter, usually I use a simple Makefile like # Variables set by the configuration script: GMX_HOME = /home/oteri/PKG/gromacs/4.5.5/gcc/ GMX_SRC = /home/oteri/PKG/sources/gromacs-4.5.5 GSL_HOME = /home/oteri/PKG//gsl/1.15/gcc MOD_HOME = /home/oteri/PKG/utilities/src MOD_BIN

Re: [gmx-users] Writing and compiling new analyses for gromacs

2012-06-04 Thread Peter C. Lai
On 2012-06-04 05:23:10PM -0400, Justin A. Lemkul wrote: > > > On 6/4/12 5:16 PM, Shay Teaching wrote: > > > > > > 2012/6/4 Justin A. Lemkul mailto:jalem...@vt.edu>> > > > > > > > > On 6/4/12 2:59 PM, Shay Teaching wrote: > > > > Dear Gromacs users, > > > > I want to write new

Re: [gmx-users] Writing and compiling new analyses for gromacs

2012-06-04 Thread Justin A. Lemkul
On 6/4/12 5:16 PM, Shay Teaching wrote: 2012/6/4 Justin A. Lemkul mailto:jalem...@vt.edu>> On 6/4/12 2:59 PM, Shay Teaching wrote: Dear Gromacs users, I want to write new analyses for gromacs and compile it (so I'll have g_whatever) as part of the gromacs pack

Re: [gmx-users] Writing and compiling new analyses for gromacs

2012-06-04 Thread Shay Teaching
2012/6/4 Justin A. Lemkul > > > On 6/4/12 2:59 PM, Shay Teaching wrote: > >> Dear Gromacs users, >> >> I want to write new analyses for gromacs and compile it (so I'll have >> g_whatever) as part of the gromacs package. >> Per the instructions I found on gromacs website, I installed kdevelop and

Re: [gmx-users] Writing and compiling new analyses for gromacs

2012-06-04 Thread Justin A. Lemkul
On 6/4/12 2:59 PM, Shay Teaching wrote: Dear Gromacs users, I want to write new analyses for gromacs and compile it (so I'll have g_whatever) as part of the gromacs package. Per the instructions I found on gromacs website, I installed kdevelop and opened the gromacs as a project using kdevelop

Re: [gmx-users] Water molecules cannot be settled, why?

2012-06-04 Thread Justin A. Lemkul
On 6/4/12 3:53 PM, John Ladasky wrote: Recently I have started to get crash messages in my molecular dynamics runs which look like this: Reading file exp37b-prep.tpr, VERSION 4.5.4 (single precision) Making 1D domain decomposition 5 x 1 x 1 starting mdrun 'Protein in water' 50 steps, 1000.

[gmx-users] Water molecules cannot be settled, why?

2012-06-04 Thread John Ladasky
Recently I have started to get crash messages in my molecular dynamics runs which look like this: Reading file exp37b-prep.tpr, VERSION 4.5.4 (single precision) Making 1D domain decomposition 5 x 1 x 1 starting mdrun 'Protein in water' 50 steps, 1000.0 ps. step 81240: Water molecule start

[gmx-users] Writing and compiling new analyses for gromacs

2012-06-04 Thread Shay Teaching
Dear Gromacs users, I want to write new analyses for gromacs and compile it (so I'll have g_whatever) as part of the gromacs package. Per the instructions I found on gromacs website, I installed kdevelop and opened the gromacs as a project using kdevelop. However I have two questions: 1) When I tr

Re: [gmx-users] Electrostatic interactions and atoms with nul charge

2012-06-04 Thread Mark Abraham
On 5/06/2012 12:08 AM, Laurence Leherte wrote: Dear Gromacs users, I am using the Amber99 FF in MD simulations of peptides (and proteins). In a first stage to the design a different charge distribution, most of the atomic charges were set equal to zero (i.e., all charges but the C and O backb

[gmx-users] Electrostatic interactions and atoms with nul charge

2012-06-04 Thread Laurence Leherte
Dear Gromacs users, I am using the Amber99 FF in MD simulations of peptides (and proteins). In a first stage to the design a different charge distribution, most of the atomic charges were set equal to zero (i.e., all charges but the C and O backbone atoms). It appeared that the calculation tim

Re: [gmx-users] Re: dangling bond at at one of the terminal ends

2012-06-04 Thread Justin A. Lemkul
On 6/4/12 7:29 AM, ramaraju801 wrote: hi, i checked the .rtp file residues such as DCN,DC5,DGN,DG5,DAN,DA5,DTN,DT5 dint have any phosphate gp but when i tested the .rtp file with a random DNA pdb file it is producing a topology file. Then you'll have to translate this newfound knowledge int

[gmx-users] Re: dangling bond at at one of the terminal ends

2012-06-04 Thread ramaraju801
hi, i checked the .rtp file residues such as DCN,DC5,DGN,DG5,DAN,DA5,DTN,DT5 dint have any phosphate gp but when i tested the .rtp file with a random DNA pdb file it is producing a topology file. -ram -- View this message in context: http://gromacs.5086.n6.nabble.com/Re-dangling-bond-at-at-o

[gmx-users] Steered MD

2012-06-04 Thread Mike M
Dear Gromacs Users, I am trying to study the conformational path from state A to state B with targeted molecular dynamics. These two states are two different structures of a peptide that I have calculated after a series of nmr experiments. I have perform 100ns simulations separately of the two pep

[gmx-users] Regarding error.

2012-06-04 Thread Seera Suryanarayana
Dear Mark, What type of file i have to check for missing of atoms. Thanks and regards. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before p

[gmx-users] Regarding error

2012-06-04 Thread Seera Suryanarayana
Dear all gromacs users, I tried the grompp and i got the following error. Fatal error: moleculetype CU1 is redefined. Is there any explanation why is thid happening? I've checked [moleculetypes] in topology files and there are not duplicated. I would appreciate any help. Iam new in using

Re: [gmx-users] How to maintain the same exact positions of the protein and ligand in the extracted frame/pdb file as they were in the trajectory form?

2012-06-04 Thread Mark Abraham
On 4/06/2012 6:18 PM, Wayne Chen wrote: Hi, I'm a student at National Taiwan University doing research on protein-ligand interactions using MD simulations with GROMACS (version 4.5.3). In our simulations, we placed a protein (group A) and a ligand (group B) in a box under periodic boundary condi

[gmx-users] How to maintain the same exact positions of the protein and ligand in the extracted frame/pdb file as they were in the trajectory form?

2012-06-04 Thread Wayne Chen
Hi, I'm a student at National Taiwan University doing research on protein-ligand interactions using MD simulations with GROMACS (version 4.5.3). In our simulations, we placed a protein (group A) and a ligand (group B) in a box under periodic boundary condition and ran for 20ns. I am trying to obt

Re: [gmx-users] Tabulated potentials for dihedrals - regd

2012-06-04 Thread Mark Abraham
On 4/06/2012 3:46 AM, ramesh cheerla wrote: Dear Gromacs experts, I am planing to use tabulated potentials for dihedral functional form Summn over 'n' 0.5*K [ ( Cos n(phi-phi0)] , Here 1<= n <= 3 . I have three different K values (i.e K1,K2,K3 ) one for eac

Re: [gmx-users] Regarding error

2012-06-04 Thread Mark Abraham
On 4/06/2012 5:05 PM, Seera Suryanarayana wrote: Dear all gromacs users, While i am running pdb2gmx commond i am getting following error. Fatal error: There were 22 missing atoms in molecule Protein_chain_A, if you want to use this incomplete topology. I w

[gmx-users] Regarding error

2012-06-04 Thread Seera Suryanarayana
Dear all gromacs users, While i am running pdb2gmx commond i am getting following error. Fatal error: There were 22 missing atoms in molecule Protein_chain_A, if you want to use this incomplete topology. I wont ignore the 22 missing atoms by using -missing commo

Re: [gmx-users] how to rename oxygen oxt to be recognized by MOLMOL

2012-06-04 Thread Mark Abraham
On 4/06/2012 5:00 PM, Acoot Brett wrote: Dear All, Will you please tell me how to rename the C-terminal residue atom OXT so that the OXT oxygen can be recognized by MOLMOL? You'd have to read the MOLMOL documentation. But start with "O" - making sure you preserve the file format correctly,

[gmx-users] how to rename oxygen oxt to be recognized by MOLMOL

2012-06-04 Thread Acoot Brett
Dear All,   Will you please tell me how to rename the C-terminal residue atom OXT so that the OXT oxygen can be recognized by MOLMOL?   Cheers,   Acoot-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gr