[gmx-users] Re:Error in trjconv

hi no exact reason, but it is a shared option, and i dont have the option to access other types. main thing to notice is, this trjconv working clearly for a protein with single chain and more this creates problem only when a ligand bound dimer is used. can you have any solution. thanks Parthiban

[gmx-users] charge density

Hello All We have tried to calculate the slab averaged charge density by adding up all the partial charges and dividing the sum by the slab volume. The charge density profile along the z axis for a single snapshot of a trajectory with our method was compared with the profile obtained from the g_po

Re: [gmx-users] generating conf.gro

Hi Tsjerk, Thank you for this suggestion. It's a good idea to have previously equilibrated bricks then used for a main system. Unfortunately, my the ratios between ion and solvent usually appear quite far from the integer because I have fixed concentration. Moreover, a CNT is present in the same

Re: [gmx-users] protein/dmso simulation

prasun kumar wrote: dear users I am trying to run the simulation fo a protein/DMSO system,Its working well till genbox but while running GROMPP I am gettin a fatal error,which is atom type 'SD' not found. SD is given in the gro & itp file of DMSO. what should I do to overcome this problem...

Re: [gmx-users] Re: gmx-users Digest, Vol 52, Issue 66

minnale wrote: Thanks Nuno for your information , the archives mentioned website about do_dssp it's not freely available program. I couldnt able to get the program, am I right Could please help me. Did you visit the website I linked in my earlier reply? DSSP is indeed free. Visit the s

[gmx-users] protein/dmso simulation

dear users I am trying to run the simulation fo a protein/DMSO system,Its working well till genbox but while running GROMPP I am gettin a fatal error,which is atom type 'SD' not found. SD is given in the gro & itp file of DMSO. what should I do to overcome this problem I have tried by repla

Re: [gmx-users] CHARMM FF

Sorry for the late answer. I wasn't in my office on the last 2 weeks. Roland Schulz wrote: On Thu, Jul 17, 2008 at 6:26 PM, Nicolas <[EMAIL PROTECTED] > wrote: We also have a implementation of CHARMM(27) for Gromacs, but without CMAP as well. How is it d

[gmx-users] Re: gmx-users Digest, Vol 52, Issue 66

Thanks Nuno for your information , the archives mentioned website about do_dssp it's not freely available program. I couldnt able to get the program, am I right Could please help me. Thanks alot >Maybe I can help with some more details. I'm sorry if my explanation is >to much detailed. > >I

RE: [gmx-users] [ atomtypes ] are not case sensitive?

Hi, In this case at least the non-bonded parameters seem to be the identical. Are there some different parameters for atom types which only differ in case? That is bad practice IMHO. But if so, we should consider changing this or adding an option. Berk. Date: Thu, 14 Aug 2008 14:41:06 +0100 Fro

[gmx-users] Out of office AutoReply

Out of office AutoReply => August the 31th For urgent matters, please contact Colette Zeches: [EMAIL PROTECTED] +32(0)81-62.25.21 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the arc

Re: [gmx-users] tfe

shahrbanoo karbalaee wrote: Dear justin as your telling I have two way for my problem: 1-choose force field that is compatible to TFE(with 7 atom) that I used another force field.I made tfe.pdb (with 7 atom) and choose gromos 96 but I got error that dont found HO atom. Are you trying to creat

[gmx-users] tfe

Dear justin as your telling I have two way for my problem: 1-choose force field that is compatible to TFE(with 7 atom) that I used another force field.I made tfe.pdb (with 7 atom) and choose gromos 96 but I got error that dont found HO atom. 2)another way,I must itp file for tfe with opls forcefiel

RE: [gmx-users] catastrophic error: "timer not defined"

Hi, Don't compile with fortran, it will not be faster. Berk. > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Date: Mon, 18 Aug 2008 15:01:27 +0400 > Subject: [gmx-users] catastrophic error: "timer not defined" > > Hello, > I am building fftw 3.0.1 with intel compilers 3.1.038 on opensu

Re: [gmx-users] temperature coupling for complex+ligand+water+ions

Alan wrote: Dears, I took a look at wikis and keep following this list but I still have doubts that I would appreciate any advice for. What would be the recommended approach for temperature coupling for a system composed of protein + ligand + water + ions? Which termostat: Berendsen or No

[gmx-users] catastrophic error: "timer not defined"

Hello, I am building fftw 3.0.1 with intel compilers 3.1.038 on opensuse 11 (Intel Core Quadro). I`ve set: export CC=path to icc export F77=path to ifort export LINKER=path to ifort ./configure --enable-float make 1/ Configure script reported two strange things. First one: configure: WARNING: lim

[gmx-users] temperature coupling for complex+ligand+water+ions

Dears, I took a look at wikis and keep following this list but I still have doubts that I would appreciate any advice for. What would be the recommended approach for temperature coupling for a system composed of protein + ligand + water + ions? Which termostat: Berendsen or Nose-Hoover? NPT by the

[gmx-users] Out of office AutoReply

Out of office AutoReply => August the 31th For urgent matters, please contact Colette Zeches: [EMAIL PROTECTED] +32(0)81-62.25.21 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the arc

[gmx-users] Out of office AutoReply

Out of office AutoReply => August the 31th For urgent matters, please contact Colette Zeches: [EMAIL PROTECTED] +32(0)81-62.25.21 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the arc

Re: [gmx-users] Error in trjconv

Hi Parthiban, Do you have a particular reason for using the MPI version of trjconv? Do you have the same error with the standard version? Cheers, Tsjerk On Mon, Aug 18, 2008 at 6:12 AM, M.Parthiban <[EMAIL PROTECTED]> wrote: > Hi > > I am encountering an error in file conversion from .trr file

Re: [gmx-users] generating conf.gro

Hi Vitaly, Do you have a rather fixed ratio between the two? ion:solvent = 1:10 e.g. Then you could make an arrangement of a single ion with surrounding solvent and replicate that with genconf. You could even do a short simulation setting rvdw to less than half the size of your small box :p for a

[gmx-users] generating conf.gro

Hi, I want to create a system (conf.gro) consisting of a solvent and polyatomic (brachiated enough) ions. Using genconf and genbox I increase the number of molecules and then ions (or contrariwise). But genbox refuses to add all the requested particles at once (because of intersections, I guess).