[gmx-users] problem with gromcas 4.5.3

2011-02-27 Thread leila separdar
I have installed gromacs version 4.5.3. when I want to use pdb2gmx for generating .top and .gro files for 1000 argon atoms, in topology file I have seen another atom O with mass 1.48594e-41 as below I do not know what to do.I do not confront with such problems when I had 4.0.7 version of gromacs.

Re: [gmx-users] problem with gromcas 4.5.3

2011-02-27 Thread Justin A. Lemkul
leila separdar wrote: I have installed gromacs version 4.5.3. when I want to use pdb2gmx for generating .top and .gro files for 1000 argon atoms, in topology file I have seen another atom O with mass 1.48594e-41 as below I do not know what to do.I do not confront with such problems when I

[gmx-users] PROCHEK-NMR instalation problem

2011-02-27 Thread najwa drici
hi all Anybody guide me in installig the PROCHECK software and how to run it ?? best regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] PROCHEK-NMR instalation problem

2011-02-27 Thread Justin A. Lemkul
najwa drici wrote: hi all Anybody guide me in installig the PROCHECK software and how to run it ?? This list is for Gromacs-related questions. Consult whatever documentation Procheck provides and make use of whatever support resources they offer. -Justin best regards --

[gmx-users] excess chemical potential

2011-02-27 Thread Thomas Koller
Hello, I want to calculate the excess chemical potential of one dissolved molecule within an liquid system. The excess chemical potential should be delta G. The equation for delta G is given in manual: With -fee an estimate is calculated for the free-energy difference with an ideal gas state:

[gmx-users] ***Extended deadline: March 18*** COMETS 2011 - 2nd International Track on Collaborative Modeling and Simulation - Call for Papers

2011-02-27 Thread Daniele Gianni
Please note submission deadline extended to March 18, 2011 (apologies if you receive multiple copies of this call for papers) # IEEE WETICE 2011 2nd International Track on Collaborative

[gmx-users] Positive potential energy in simulation using polarizable model

2011-02-27 Thread aldi asmadi
Dear all, This may sound obvious and normally I would know how to address the following question. However, I would like to ask for your opinion. If we are simulating bulk liquid of hydrocarbon using the shell polarizable model, is it possible to have a positive value for the potential energy?

Re: [gmx-users] Positive potential energy in simulation using polarizable model

2011-02-27 Thread David van der Spoel
On 2011-02-27 21.20, aldi asmadi wrote: Dear all, This may sound obvious and normally I would know how to address the following question. However, I would like to ask for your opinion. If we are simulating bulk liquid of hydrocarbon using the shell polarizable model, is it possible to have a

Re: [gmx-users] Positive potential energy in simulation using polarizable model

2011-02-27 Thread aldi asmadi
Many thanks David. Just want to confirm that I understand how to calculate the monomer correctly. So I put the single molecule inside a large cubic box, say with a dimension of 10 x 10 x 10 nm^3, then I use NVT ensemble and the same cut-off parameters as the ones that I apply during my bulk

Re: [gmx-users] Positive potential energy in simulation using polarizable model

2011-02-27 Thread David van der Spoel
On 2011-02-27 21.49, aldi asmadi wrote: Many thanks David. Just want to confirm that I understand how to calculate the monomer correctly. So I put the single molecule inside a large cubic box, say with a dimension of 10 x 10 x 10 nm^3, then I use NVT ensemble and the same cut-off parameters as

[gmx-users] Re: Enquire about double strand DNA in gmx 4.5.3 charmm27 ff.Thank you.

2011-02-27 Thread Justin A. Lemkul
Please keep all Gromacs-related correspondence on the gmx-users list. I am not a private tutor. I am CC'ing your message to the list and would ask that all further discussion be sent there. See comments below. Yanping Fan, Liza (Dr) wrote: Dear Justin: Good day. I found your

[gmx-users] .tdr file not created

2011-02-27 Thread sakthi kumaran
hi I installed gromacs through the synaptics package manager in ubuntu 10.10 Since I am new to linux. So after installation when I tried to run the example tutorials available in tutor folder, its not running. When I tried to run the program water the .tdr file is not created while executing

Re: [gmx-users] about -CN triple bond

2011-02-27 Thread C.Y. Chang
Hi, I try to add a dummy atom in my small molecular pdb and topology file. (attached files) But the MDS process still shut down. The msg. is [1]+ Exit 255nohup mdrun -v -deffnm npt_cmplx Could you give me some suggestions for dealing with the problem. Thaks a lot. Best,