[gmx-users] Re: gmx-users Digest, Vol 48, Issue 54

s configured for 64 bit with ELF > format but still getting same error of libmpi.so.0 not found while > performing GDB serial debugging with single node. > > Note: I had performed GDB debugging for small MPI program(hello world) > using > OpenMPI(v1.2.5/v1.2.6) wthout GROMACS associati

Re: [gmx-users] dielectric constant

Mark Abraham wrote: [EMAIL PROTECTED] wrote: Hello, I'm interested in running a simulation in which the box will be divided in to two different dielectric constants separated at a plane. Is it possible to do that in Gromacs? Possible, yes. However it is not implemented, and it is not a tri

Re: [gmx-users] acetone parameter

Mark Abraham wrote: JMandumpal wrote: Dear list, I would like to simulate aqueous acetone system using UA OPLS potentials. I chose the following atoms types, given below (TABLE ONE), for acetone, with united atom for Methyl groups. TABLE ONE ---

Re: [gmx-users] acetone parameter

JMandumpal wrote: Dear list, I would like to simulate aqueous acetone system using UA OPLS potentials. I chose the following atoms types, given below (TABLE ONE), for acetone, with united atom for Methyl groups. TABLE ONE

[gmx-users] acetone parameter

Dear list, I would like to simulate aqueous acetone system using UA OPLS potentials. I chose the following atoms types, given below (TABLE ONE), for acetone, with united atom for Methyl groups. TABLE ONE

Re: [gmx-users] hydrogen bonds of peptide with lipids

maria goranovic wrote: Yes, I am using united atoms. I am looking for H-bonds between phosphate groups of lipids and the H-bonding atoms of the protein. i have used g_hbond to find the relevant intra-protein H-bonds, but need to find protein-lipid H-bonds. I tried using g_hbond, using the pro

Re: [gmx-users] water in channel by "Dowser"

Hero wrote: Dear Gramacs, Anybody know where I can get "Dowser" for water in channel? No, but Google does. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http:/

Re: [gmx-users] Conformation search!

Anthony Cruz wrote: Hi User: We have a protein with two domains. This two domains were connected by two linkers of different length. We want to study the different conformation that the protein domains can adopt depending the length of the linkers without loosing the secondary structure featur

Re: [gmx-users] dielectric constant

[EMAIL PROTECTED] wrote: Dear Mark, Please leave traffic on the list for all to learn from and so that the conversation gets archived. Is there somewhere I can read about this? Not that I know of. Do you have an example of a similar simulation that has been done? No. I was commenting

[gmx-users] water in channel by "Dowser"

Dear Gramacs, Anybody know where I can get "Dowser" for water in channel? Thanks a lot! [gmx-users] water in channel Eric Jakobsson jake at ncsa.uiuc.edu Mon Jan 19 22:50:02 CET 2004 Previous message: [gmx-users] water in channel Next message: [gmx-users] water in channel Messages sorted by:

[gmx-users] water flow in CNT

Dear All, I am simulating water transport in CNT under pressure. If I use periodic boundary conditions, how can I scale the water velocity? Otherwise the velocity will be going to heaven! Thank you very much! Hero

Re: [gmx-users] query about .xpm file

Bert wrote: Hi gmx-usrs, I use the program g_densmap to generate a xpm file, and then I convert it to eps format with xpm2ps. It goes quite well except for the illegible coordinates with the ticks. I wonder if I can set those coodinates arbitrarily. I have tried to adjust the -bx, -by set an

[gmx-users] Conformation search!

Hi User: We have a protein with two domains. This two domains were connected by two linkers of different length. We want to study the different conformation that the protein domains can adopt depending the length of the linkers without loosing the secondary structure feature present. I was think

Re: [gmx-users] epsilon in mdp

Vitaly Chaban wrote: Dear gromacs users, In the gromacs example mdp-file for water (/tutor/water) one can find " ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r = 1 " Does it mean that the simulation will be hold as if DC of H2O were equal to the DC of vacuum? Does one

Re: [gmx-users] GDB Debugging - GROMACS(v-3.3.3) Application with OpenMPI(v-1.2.5/v-1.2.6)

Mukesh K Srivastava wrote: Hi. Anyone had performed GDB debugging for Gromacs(v3.x - v3.3.3) application with FFTW(v3.1) using OpenMPI(v-1.2.5 or v-1.2.6). I had properly configured OpenMPI with debug option and also configured Gromacs alongwith FFTW succesfully. I can perform p2bdbx_mpi, e

[gmx-users] GDB Debugging - GROMACS(v-3.3.3) Application with OpenMPI(v-1.2.5/v-1.2.6)

Hi. Anyone had performed GDB debugging for Gromacs(v3.x - v3.3.3) application with FFTW(v3.1) using OpenMPI(v-1.2.5 or v-1.2.6). I had properly configured OpenMPI with debug option and also configured Gromacs alongwith FFTW succesfully. I can perform p2bdbx_mpi, editconf_mpi, genbox_mpi, grompp_mp

Re: [gmx-users] hydrogen bonds of peptide with lipids

Yes, I am using united atoms. I am looking for H-bonds between phosphate groups of lipids and the H-bonding atoms of the protein. i have used g_hbond to find the relevant intra-protein H-bonds, but need to find protein-lipid H-bonds. I tried using g_hbond, using the protein and POPC as the two gro

[gmx-users] hydrogen bonds of peptide with lipids

Are you using united atom lipids? If so, you may want to reconsider attempting this. If not, you'll be more likely to get further assistance if you provide quite a bit more information and demonstrate that you invested some time trying to solve this. -- original message -- Yes, I looked in

[gmx-users] query about .xpm file

Hi gmx-usrs, I use the program g_densmap to generate a xpm file, and then I convert it to eps format with xpm2ps. It goes quite well except for the illegible coordinates with the ticks. I wonder if I can set those coodinates arbitrarily. I have tried to adjust the -bx, -by set and the m2p input fi

Re: [gmx-users] Concatenate TPR files after restart

Quoting Ricardo Soares <[EMAIL PROTECTED]>: > Hello everyone, > > I've extended one previously finished simulation from 5 ns to 10 ns. Now > I have two tpr files. How can I merge both of them in only one file? > I'm asking this because I need to use g_hbond and I wanna analyze the > whole trajecto

[gmx-users] Concatenate TPR files after restart

Hello everyone, I've extended one previously finished simulation from 5 ns to 10 ns. Now I have two tpr files. How can I merge both of them in only one file? I'm asking this because I need to use g_hbond and I wanna analyze the whole trajectory. Best regardings. -- __

[gmx-users] epsilon in mdp

Dear gromacs users, In the gromacs example mdp-file for water (/tutor/water) one can find " ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r = 1 " Does it mean that the simulation will be hold as if DC of H2O were equal to the DC of vacuum? Does one need to correct it to t

Re: [gmx-users] hydrogen bonds of peptide with lipids

Quoting maria goranovic <[EMAIL PROTECTED]>: > Yes, I looked into that. But could not find any information about how to > include new acceptor or donor atoms. Could you please be more specific ? > Thank you ! These are probably defined in the source code, but I'll admit that I have never gone loo

Re: [gmx-users] about fourier grid

Hi Anamika, if you use Particle-Mesh-Ewald (PME) electrostatics these parameters are used to control the (discrete) grid layout onto which the electrostatic charges are extrapolated (from their continuous positions). The basic value of 0.12 nm for the fourierspacing means that you will have a PM

Re: [gmx-users] FW: dynamic of a peptide in a mixture TFE/H2O ( 30/70 %)

Quoting Luisa Calvanese <[EMAIL PROTECTED]>: > > > > > I'm doing a dynamic of a peptide in a mixture TFE/H2O ( 30/70 %).I'm using > this file.mdp : cpp = /lib/cppdefine = -DFLEX_SPC -DPOSRESconstraints = > all-bondsintegrator = mdtinit = 0.0dt = 0.002 ; ps !nsteps = 50 ; total > 1000 ps.nstcom

Re: [gmx-users] dielectric constant

[EMAIL PROTECTED] wrote: Hello, I'm interested in running a simulation in which the box will be divided in to two different dielectric constants separated at a plane. Is it possible to do that in Gromacs? Possible, yes. However it is not implemented, and it is not a trivial change to do so

[gmx-users] FW: dynamic of a peptide in a mixture TFE/H2O ( 30/70 %)

I'm doing a dynamic of a peptide in a mixture TFE/H2O ( 30/70 %).I'm using this file.mdp : cpp = /lib/cppdefine = -DFLEX_SPC -DPOSRESconstraints = all-bondsintegrator = mdtinit = 0.0dt = 0.002 ; ps !nsteps = 50 ; total 1000 ps.nstcomm = 1nstxout = 1000nstvout = 1000nstfout = 0nstxtcout =

Re: [gmx-users] about fourier grid

Anamika Awasthi wrote: Dear Gromacs user, Please tell me what is the significance of fourier grid and spacing in MD simulation? Search for "Fourier" in the manual. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mai

Re: [gmx-users] reg hybrid dynamics

vidhya sankar wrote: dear sir, what should i do to do hybriddunamics during installation of Gromacs . that is i* am asking about technical implementation of QM/MM in gromacs thanks in advance i am expecting your reply soon * Please make an effort to write in more correct En

[gmx-users] dielectric constant

Hello, I'm interested in running a simulation in which the box will be divided in to two different dielectric constants separated at a plane. Is it possible to do that in Gromacs? Thanks in advance This message was sent using

Re: [gmx-users] hydrogen bonds of peptide with lipids

Yes, I looked into that. But could not find any information about how to include new acceptor or donor atoms. Could you please be more specific ? Thank you ! On Thu, Apr 17, 2008 at 12:34 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > Quoting maria goranovic <[EMAIL PROTECTED]>: > > > Dear All

[gmx-users] about fourier grid

Dear Gromacs user, Please tell me what is the significance of fourier grid and spacing in MD simulation? Thanks in advance ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] reg hybrid dynamics

dear sir, what should i do to do hybriddunamics during installation of Gromacs . that is i am asking about technical implementation of QM/MM in gromacs thanks in advance i am expecting your reply soon - Share files, take polls, and ma

Re: [gmx-users] hydrogen bonds of peptide with lipids

Quoting maria goranovic <[EMAIL PROTECTED]>: > Dear All, > > Where are the donor and acceptor atoms defined for the g_hbond analysis ? I > was trying to calculate h-bonds between a peptide and a popc bilayer, but > there are no acceptor or donors listed for POPC. How can one change this ? Have a

[gmx-users] hydrogen bonds of peptide with lipids

Dear All, Where are the donor and acceptor atoms defined for the g_hbond analysis ? I was trying to calculate h-bonds between a peptide and a popc bilayer, but there are no acceptor or donors listed for POPC. How can one change this ? Sincerely, -Maria -- Maria G. Technical University of Denmar

[gmx-users] Re: Wrong heat capacity (water)

Continuation of thread http://www.gromacs.org/index.php?option=com_wrapper&Itemid=84 (answered by David van der Spoel) >> Hello all, >> >> I ran a MD simulation of TIP4P water in the NVT ensemble (976 molecules, >> density=0.98 g/cm3, T=300K (Nose-Hoover), SETTLE and PME enabled). This >> work

Re: [gmx-users] GTP in topology

Quoting s lal badshah <[EMAIL PROTECTED]>: > Hi All, > I have taken the GTP topology from PRODRG server but now how can I make a > connection with my original topology file: As in Errors of Gromacs it is > mentioned > > ==> find a topology file for the residue / molecule and include as a .itp > fi

[gmx-users] Re: Where can I find structure files of water and CNT?

Please keep all correspondence on the gmx-users listserv; that way everything that is said can be archived for everyone's future use. I personally have never worked with CNT, but I know it is frequently discussed across the list and I have seen the link to the web server. That's a good indicatio

Re: [gmx-users] GTP in topology

s lal badshah wrote: Hi All, I have taken the GTP topology from PRODRG server but now how can I make a connection with my original topology file: As in Errors of Gromacs it is mentioned ==> find a topology file for the residue / molecule and

Re: [gmx-users] GTP in topology

It means: Include the topology, you got from the PRODRG server as an itp file in your general topology file If you don't know, what I mean, read the manual about including topologies... Btw, more info, more answer regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical C

[gmx-users] GTP in topology

Hi All, I have taken the GTP topology from PRODRG server but now how can I make a connection with my original topology file: As in Errors of Gromacs it is mentioned ==> find a topology file for the residue / molecule and include as a .itp file, what does it means? I am using OPLS/aa force field