Re: [gmx-users] Monte Carlo with Gromacs and implicit solvent

Grompy looks like fancy. Is it reliable for conducting GCMC?? I also need to perform GCMC along with MD. In Grompy, it seems that the Grompy is compatible with gromacs 4.0.5. The version of gromacs I use is 4.5.X. Is it possible to use Grompy with my Gromacs?? 2012/1/25 Gianluca Interlandi >

Re: [gmx-users] protein in solution

Yao Yao wrote: Hi Gmxers, I plan to simulate a protein in an 1M glycerol solution. How can I control the concentration and "insert" the protein into my solution. Have a look at: http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents -Justin -- =

[gmx-users] protein in solution

Hi Gmxers, I plan to simulate a protein in an 1M glycerol solution. How can I control the concentration and "insert" the protein into my solution. Thanks, Yao  -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] Re: installation problem

Problem solved issue with double and single precision versions of gromacs and fftw. Ramon On Tue, Jan 24, 2012 at 2:16 PM, Jose Tusell wrote: > Hi All, > > I've installed fftw-3.3 on my computer when I try to install GROMACS I run > into problems. > > A little information: > > Here are the valu

[gmx-users] installation problem

Hi All, I've installed fftw-3.3 on my computer when I try to install GROMACS I run into problems. A little information: Here are the values for LDFLAGS and CPPFLAGS echo $LDFLAGS -L/home/ramone/mygromacs/lib The content of this directory is the following: libfftw3f.a libfftw3f.la* pkgconfig

Re: [gmx-users] Monte Carlo with Gromacs and implicit solvent

Hi Renè, This might be a silly question. In the documentation of GromPy it says that: "The system consists of mono-atomic water molceules defined in the MARTINI force field. The intermolecular interactions between such molecules are modelled using the Lennard-Jones potential only." My syst

Re: [gmx-users] Monte Carlo with Gromacs and implicit solvent

Thanks Renè and Mark, I will look at both options, GromPy and mdrun -rerun. Gianluca On Tue, 24 Jan 2012, René Pool wrote: By the way, the tutorial can be found on the wiki page at https://github.com/GromPy/GromPy/wiki/Tutorial:-Using-GromPy-in-GCMC-mode.

Re: [gmx-users] pdb2gmx changes conformation?

Hi Igor, Please look at the contents of the files. Note the order of atoms. Cheers, Tsjerk On Jan 24, 2012 7:31 PM, "192.168.100.1" wrote: ** Hi, I applied *pdb2gmx* to PDB file *A.pdb* with force field *gromos53a5* and water model *spc* and then compared the resulting *A.gro* file with ini

[gmx-users] pdb2gmx changes conformation?

Hi, I applied pdb2gmx to PDB file A.pdb with force field gromos53a5 and water model spc and then compared the resulting A.gro file with initial PDB one, using program g_rmsdist by the following command: /opt/software/gromacs/gromacs-4.5.3-intel/bin/g_rmsdist -f A.gro -s /home/shch406/PDB/A.pd

Re: [gmx-users] -fitall option problems

Oh, Justin's right. So I was wrong in my first mail, as well as in my mental picture... So fitting all to all is default... Terribly sorry :$ Tsjerk On Jan 24, 2012 12:05 PM, "Justin A. Lemkul" wrote: Víctor wrote: > > I've having some problems with use of the option '-fitall'. > > The command

Re: [gmx-users] getting started with gromacs

kumud agarwal wrote: I want to do energy minimization of a small peptide (19 residues long) file (in pdb format). Can you please tell which tutorial is best for this purpose and which force field should I use. Any of these should be fine: http://www.gromacs.org/Documentation/Tutorials#G

Re: [gmx-users] getting started with gromacs

I want to do energy minimization of a small peptide (19 residues long) file (in pdb format). Can you please tell which tutorial is best for this purpose and which force field should I use. Thanks Kumud Agarwal On Tue, Jan 24, 2012 at 10:43 AM, Justin A. Lemkul wrote: > > > kumud agarwal wrot

Re: [gmx-users] getting started with gromacs

kumud agarwal wrote: I tried to use the command pdb2gmx *kumud@ubuntu:~/gromacs/gromacs-4.5.5/share/tutor/mciz$ pdb2gmx -ignh -ff G43a1 -f mciz.pdb -o mciz.gro -p mciz.top* At the end the message came as *Program pdb2gmx, VERSION 4.5.5 Source code file: pdb2top.c, line: 239 Fatal error:

Re: [gmx-users] getting started with gromacs

I tried to use the command pdb2gmx *kumud@ubuntu:~/gromacs/gromacs-4.5.5/share/tutor/mciz$ pdb2gmx -ignh -ff G43a1 -f mciz.pdb -o mciz.gro -p mciz.top* At the end the message came as *Program pdb2gmx, VERSION 4.5.5 Source code file: pdb2top.c, line: 239 Fatal error: Could not find force field

Re: [gmx-users] getting started with gromacs

kumud agarwal wrote: How can I check if Gromacs is properly installed on my system (ubuntu)? http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation Then try any of the commands. -Justin On Tue, Jan 24, 2012 at 9:22 AM, Justin A. Lemkul

Re: [gmx-users] getting started with gromacs

How can I check if Gromacs is properly installed on my system (ubuntu)? On Tue, Jan 24, 2012 at 9:22 AM, Justin A. Lemkul wrote: > > > kumud agarwal wrote: > >> hi >> >> I am very new to Gromacs. >> >> To start working with Gromacs in which directory do I have to keep the >> pdb file that I am w

Re: [gmx-users] Installing & uninstalling of gromacs

Spring buds wrote: Removing files in /usr/local/gromacs has no bearing on the contents of /usr/local/bin. If you did 'make links' at the end of the installation, you will have dead links in /usr/local/bin that need to be removed, as well. -Justin Dear Justin, Thanks a

Re: [gmx-users] getting started with gromacs

kumud agarwal wrote: hi I am very new to Gromacs. To start working with Gromacs in which directory do I have to keep the pdb file that I am working on? You put files in whichever directory you want to do your work (provided you have sufficient permission to write in that directory). -

[gmx-users] getting started with gromacs

hi I am very new to Gromacs. To start working with Gromacs in which directory do I have to keep the pdb file that I am working on? Thanks Kumud -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs

Re: [gmx-users] Installing & uninstalling of gromacs

> Removing files in /usr/local/gromacs has no bearing on the contents of > /usr/local/bin. If you did 'make links' at the end of the installation, > you will have dead links in /usr/local/bin that need to be removed, as well. > > -Justin > Dear Justin, Thanks a lot for your insight. I did link

Re: [gmx-users] -fitall option problems

Víctor wrote: I've having some problems with use of the option '-fitall'. The command I'm using is: g_rms -hidden -fitall -s ../topol_amber.tpr -f ../amber99sb_skip10.xtc -f2 ../amber99sb_skip10.xtc -m rmsd.xpm But a diff with the rmsd.xpm file I got without using '-fitall' reveals that th

Re: [gmx-users] Installing & uninstalling of gromacs

Spring buds wrote: On Tue, Jan 24, 2012 at 11:49 AM, lina > wrote: On Tue, Jan 24, 2012 at 11:42 AM, Spring buds mailto:winterho...@gmail.com>> wrote: > Hi lina, > > Thanks for reply. could you tell me how to remove completly the gromac

[gmx-users] -fitall option problems

I've having some problems with use of the option '-fitall'. The command I'm using is: g_rms -hidden -fitall -s ../topol_amber.tpr -f ../amber99sb_skip10.xtc -f2 ../amber99sb_skip10.xtc -m rmsd.xpm But a diff with the rmsd.xpm file I got without using '-fitall' reveals that the files are identical

Re: [gmx-users] problem in generation of tpr file

On 24/01/2012 9:24 PM, Anushree Tripathi wrote: I have replaced all HW by H in ffnonbonded.itp.After executing the command: grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr I am getting this error: File input/output error: dppc128.gro This file likely does not exist. Use a file

[gmx-users] h-bonds constraints for DPPC sim?

Hi It was mentioned here http://lists.gromacs.org/pipermail/gmx-users/2011-May/061475.html that the constraints option may have to be set to h-bonds to get the exp APL in DPPC equilibration/simulation. Is this indeed true and if so how important is it for membrane/protein simulations? Thanks in

Re: [gmx-users] problem in generation of tpr file

I have replaced all HW by H in ffnonbonded.itp.After executing the command: grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr I am getting this error: File input/output error: dppc128.gro should I replace all HW with H (without delecting numbers that is given in dppc128.pdb alongwit

Re: [gmx-users] a query

On 24/01/2012 8:58 PM, Anik Sen wrote: Thanx Mark. I understand that I have to change the residue names. But how to generate them. Is there any software by which I can generate or any sequence by which I may change them.. Only your text editor. Wherever you got your coordin

RE: [gmx-users] a query

Thanx Mark. I understand that I have to change the residue names. But how to generate them. Is there any software by which I can generate or any sequence by which I may change them.. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromac

Re: [gmx-users] a query

On 24/01/2012 8:32 PM, Anik Sen wrote: Hello Anik here. I think its a silly question but, could not stop to ask as its between me and my gromacs job. I am using gromacs 4.5.5. I want to run a dynamics run with DNA. I made a pdb file from vmd software. But the residue file its showing is "MOL"

[gmx-users] a query

Hello Anik here. I think its a silly question but, could not stop to ask as its between me and my gromacs job. I am using gromacs 4.5.5. I want to run a dynamics run with DNA. I made a pdb file from vmd software. But the residue file its showing is "MOL". There is no residue type named mol. So

Re: [gmx-users] Monte Carlo with Gromacs and implicit solvent

On 24/01/2012 12:39 PM, Gianluca Interlandi wrote: Hi! I would like to use gromacs to perform Monte Carlo simulations in implicit solvent of a protein near a surface. The protein is treated as a rigid body whereas the surface is fix. I see that there are plans to code MC into gromacs: http:

Re: [gmx-users] Monte Carlo with Gromacs and implicit solvent

On 24/01/2012 3:29 PM, Rodrigo Faccioli wrote: Hi Gianluca, I forgot to say that the step of compute the energies is considered from pdb2gmx until g_energy. If your topology is not changing, then you need only construct a new pseudo-trajectory for the n configurations whose energy you want,

Re: [gmx-users] regarding boxtype and numer of solvent molecules..

On 24/01/2012 3:47 PM, priya thiyagarajan wrote: hello sir, Thanks for your kind reply.. 15 boxtype accomodates 105046 solvent molecules.. Hence why adding a maximum of 5 solvent molecules left lots of empty space. but i need to run simulation by keeping number of water molecules co

Re: [gmx-users] Monte Carlo with Gromacs and implicit solvent

By the way, the tutorial can be found on the wiki page at https://github.com/GromPy/GromPy/wiki/Tutorial:-Using-GromPy-in-GCMC-mode. = René Pool Division of Molecular and Computational Toxicology Department of Chemistry and Pharmaceutical Scien

RE: [gmx-users] Monte Carlo with Gromacs and implicit solvent

Hi Gianluca, You might want to take a look at GromPy (https://github.com/GromPy/GromPy). This is a python interface to the GROMACS library. Amongst other applications, there is an option to perform grand-canonical Monte Carlo using GromPy. The necessary energy evaluations are performed using dir