Re: [gmx-users] Force vs distance plot in pulling simulation?

2012-11-17 Thread Erik Marklund
16 nov 2012 kl. 22.42 skrev Justin Lemkul: On 11/16/12 10:45 AM, Gmx QA wrote: Hello gmx-users, I've performed a pulling simulation and obtained a force-vs-time plot and a distance-vs-time plot (xvg-files). Is it common to somehow combine these to get a force-vs-distance-plot using a

RE: [gmx-users] Pull code, Velocity distribution

2012-11-17 Thread Samadashvili Nino
Hello, Sorry for bothering you with the same question but just want to make sure that I am getting my results correctly. I run simulations where two blocks of ice are in a sliding contact for 5 ns (using pull code). As an output of the simulation I have pullf.xvg file which I use for

[gmx-users] Re: Force vs distance plot in pulling simulation?

2012-11-17 Thread Gmx QA
Hi Erik and Justin Thanks, writing such a script is easy. The point of it all would be to be able to map the magnitude of the pulling force to what I see happen in the pulling simulation. How else would you get an understanding of what the pulling force means? Thanks /PK The only solution

[gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus

2012-11-17 Thread Atila Petrosian
Hi all. After using amber03 force field for protein-ligand simulation (pdb2gmx), I encountered with following error: Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus. Ligand in my system is a single residue (GLN). There are [GLN], [NGLN] and

Re: [gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus

2012-11-17 Thread David van der Spoel
On 2012-11-17 15:37, Atila Petrosian wrote: Hi all. After using amber03 force field for protein-ligand simulation (pdb2gmx), I encountered with following error: Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus. Ligand in my system is a single

Re: [gmx-users] simulation with two different force fields

2012-11-17 Thread Justin Lemkul
On 11/17/12 10:19 AM, shahab shariati wrote: Dear gromacs users Can I use two different force fields for a system with 2 components (dna and carbon nano tube)? No. Mixing and matching force fields (even if syntactically possible in the topology) invalidates the force field models.

Re: [gmx-users] simulation with two different force fields

2012-11-17 Thread Justin Lemkul
On 11/17/12 10:37 AM, shahab shariati wrote: Dear Justin Thanks for your attention. You are right but is there a force field which be appropriate for both of protein and carbon nano tube or dna and carbon nano tube? What does your search of the literature tell you? -Justin --

Re: [gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus

2012-11-17 Thread David van der Spoel
On 2012-11-17 16:26, Atila Petrosian wrote: Dear David Thanks for your quick reply. You said Add an alanine after the gln then in the top file rename and remove atoms. I confused. Why ALA? ALA (alanine) is a residue which is very simple than GLN structurally. I should add alanine after the

[gmx-users] (no subject)

2012-11-17 Thread behnoosh Bahadori
-- 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 posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to