[gmx-users] Re: gmx-users Digest, Vol 89, Issue 83

Hello GMX users, I have a couple of questions regrading energy run and g_lie: 1. I am interested in calculating the estimated binding energy between pip2 and a protein using the lie method. 2. I have run the protein ligand complex for 40 ns with counter-ions, npt ensemble and PME 3. In order to

[gmx-users] regarding energy run and g_lie

בתאריך 15 בספטמבר 2011 12:58, מאת גדעון לפידות glapid...@gmail.com: Hello GMX users, I have a couple of questions regrading energy run and g_lie: 1. I am interested in calculating the estimated binding energy between pip2 and a protein using the lie method. 2. I have run the protein ligand

Re: [gmx-users] Re: amb2gmx.pl to convert GLYCAM topology

Thanks Yun, Have a look at http://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx so you may have tips of how to improve you check. One thing I recorded that makes diff is that amber input files have 6 decimals of precision and PDB/GRO only 3. Not knowing exactly what you did, but it sounds

Re: [gmx-users] radial distribution function

Hello again, I tried comparing RDF plots generated by sampling from 4 to 5 ns run and a longer run from 4 to 30 ns to see whether the small jumps on the plot are due to insufficient sampling. Attached is the new plot showing that two RDF curves are almost identical. I only wanted to let you know

[gmx-users] Free energy sampling using G_bar

Hello all, I am finished running a free energy calculation using g_bar and i followed Justin Lemkuls tutorial and I am in the process of analyzing inorder to determine if I had adequate sampling.  I have read the 'BAR' paper by Bennett but there are still some concerns whether I have enough

Re: [gmx-users] Free energy sampling using G_bar

Fabian Casteblanco wrote: Hello all, I am finished running a free energy calculation using g_bar and i followed Justin Lemkuls tutorial and I am in the process of analyzing inorder to determine if I had adequate sampling. I have read the 'BAR' paper by Bennett but there are still some

[gmx-users] Counting non-bonding interaction

Hi Is there any function counting non-bonding interaction with Gromacs ? Thanks Lin -- 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

Re: [gmx-users] Counting non-bonding interaction

Chih-Ying Lin wrote: Hi Is there any function counting non-bonding interaction with Gromacs ? You got a response to this question already: http://lists.gromacs.org/pipermail/gmx-users/2011-September/064299.html Please be more specific. -Justin --

Re: [gmx-users] simulation with amber10 and gromacs 4.5.1

Hey vrk. You should carefully compare all run parameters that were active in either program. Sending the parameter files to the list might raise some useful suggestions. Cheers, Tsjerk On Sep 14, 2011 3:53 PM, Justin A. Lemkul jalem...@vt.edu wrote: vijayaraj ramadoss wrote: Hello Users,

Re: [gmx-users] V(R) around protein

Hey Mark, Nihal, On Tue, Sep 13, 2011 at 2:06 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 13/09/2011 9:47 AM, E. Nihal Korkmaz wrote: And I don't think g_sas would do what i want. It calculates the volume of the protein itself. I am interested in the V of space at a distance R from

Re: [gmx-users] Re: g_sas of ligands

Hey, The protein-buried hydrophobic area will only be considered if you use a combined group comprising ligands and protein to calculate the surface (and ligands only for output). If you use ligand only as group for calculation and for output, you'll only get the area buried between ligands.

RE: [gmx-users] radial distribution function

Load up some frames into VMD and start measuring the distances shown by the peaks in your RDF, link them with what you actually see in there (using something like a transparent representation of the carbon atom(s) using VDW then set the sphere scale so that it matches the correct radius, may be

Re: [gmx-users] radial distribution function

Hey, This is just exactly what you'd expect for polymer chains in a solution (suspension?). From the closest neighbours the fine structure, the discrete distribution of carbon atoms, is still seen, but for those further away it's blurred. Dallas' excercise should be a fine way to show that more

[gmx-users] residue numbering different

Hi Users, When i list the residues in a index file it shows a numbering of residues and when open the same protein in VMD and check the residue numbering its different. i want to visualise the protein in VMD and select a residue number from VMD and use in gromacs ie want to make an index file in

Re: [gmx-users] residue numbering different

The first residue number in VMD is 0, not 1. Jianguo From: aiswarya pawar aiswarya.pa...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 16 September 2011 1:21 PM Subject: [gmx-users] residue numbering different Hi Users,