[gmx-users] farticle demanding about Small-Molecule Topologies

Dear Dr.Lemkul would you please send me full text of your below article : Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies unfortunately, i dont have accessible to full text of this article thanks a lot -- Gromacs Users mailing list * Please search the archive

[gmx-users] how to remove water molecule inside micelle

Hello, It is not a really problem, since the water will move during the simulation (due to the hydrophobic effect), but It may take for that all the water left the micelle center. So I suggest you to use genbox with the following arguments -shell or -vdwd (see the genbox manual). An other

[gmx-users] -vsite hydrogen

Dear Users, I am simulating a membrane protein with charmm ff with a 2fs time step. How the results will be affected if I use a 5fs time step by using -vsite hydrogen option in pdb2gmx? Do my results loose their accuracy if I use this option? Best wishes, H.A -- Gromacs Users mailing list *

[gmx-users] Obtaining PMF for change in domain position

Hello GROMACS Users, This is a problem I am facing for the first time. Kindly guide be to the best options. I have a protein which has two large domains connected by a flexible linker peptide (~10 aa). The two domains seem to interact with each other and have been crystallized in three different

Re: [gmx-users] how to remove water molecule inside micelle?

it's hard to say without knowing how you prepared and relaxed your micelle before adding water, so I can only provide you a few general comments: (1) a properly relaxed, well-packed micelle should not present any voids and water should not go inside the micelle (check the literature, this has

Re: [gmx-users] charge distribution

On 12/29/14 2:31 AM, elham tazikeh wrote: Dear Justin i really appricite for your help i want to tell all did work until now, again: 1.total charges in my topol.top was +2, then by genion, i added 2 CL to my comlex (HSA+Aspirin) 2.My .itp file (produce by PRODRG) was(consist of 11 atoms) :

Re: [gmx-users] farticle demanding about Small-Molecule Topologies

On 12/29/14 3:56 AM, elham tazikeh wrote: Dear Dr.Lemkul would you please send me full text of your below article : Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies unfortunately, i dont have accessible to full text of this article thanks a lot Contact me

Re: [gmx-users] -vsite hydrogen

On 12/29/14 6:28 AM, h.aliza...@znu.ac.ir wrote: Dear Users, I am simulating a membrane protein with charmm ff with a 2fs time step. How the results will be affected if I use a 5fs time step by using -vsite hydrogen option in pdb2gmx? Do my results loose their accuracy if I use this option?

Re: [gmx-users] Obtaining PMF for change in domain position

On 12/29/14 6:57 AM, Abhi Acharya wrote: Hello GROMACS Users, This is a problem I am facing for the first time. Kindly guide be to the best options. I have a protein which has two large domains connected by a flexible linker peptide (~10 aa). The two domains seem to interact with each other

[gmx-users] pdb information

Dear GMX users i d like to know about pdb information for instance, when i defined concentration of an ion by genion (-conc), gromacs added ion(s) to my structure Now, my question is: in a pdb e.g. (1ZE9: Amyloid beta peptide+Zn+2), there is only one cation in pdb file i want to know about its

Re: [gmx-users] pdb information

On 12/29/14 11:08 AM, elham tazikeh wrote: Dear GMX users i d like to know about pdb information for instance, when i defined concentration of an ion by genion (-conc), gromacs added ion(s) to my structure Now, my question is: in a pdb e.g. (1ZE9: Amyloid beta peptide+Zn+2), there is only

Re: [gmx-users] Obtaining PMF for change in domain position

On Mon, Dec 29, 2014 at 8:59 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/29/14 6:57 AM, Abhi Acharya wrote: Hello GROMACS Users, This is a problem I am facing for the first time. Kindly guide be to the best options. I have a protein which has two large domains connected by a flexible

[gmx-users] Gromacs error regarding default gromos bond type and angle type

Dear Gromacs users we want to simulate 1EA1 pdf file using gromacs. (according to justin tutorial). This pdf file contains two cofactors including TPF and HEM. Our next step is to dock some antifungal drugs to this protein which is cytochrome of the fungi. As the TPF was not located in the

[gmx-users] Fw: Gromacs error regarding default gromos bond type and angle type

Dear Gromacs users we want to simulate 1EA1 pdf file using gromacs. (according to justin tutorial). This pdf file contains two cofactors including TPF and HEM. Our next step is to dock some antifungal drugs to this protein which is cytochrome of the fungi. As the TPF was not located in the

Re: [gmx-users] -vsite hydrogen

We have tested virtual sites with CHARMM36 lipids; straightforward usage gives too ordered membranes. We have created custom virtual sites construction for lipid hydrogens and used them for pure membranes as well as for membrane proteins, and the differences between membrane properties with

[gmx-users] charge distribution

Dear Justin thanks a lot for your response, your answers were very clear As you said,for building blocks i cant use of protein force field and i have to get from the literature(s) would you please recommend me some literature that i can use them? cheers -- Gromacs Users mailing list * Please

[gmx-users] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3)

Dear gromacs users, I just recently bought a workstation that posees two GTX 980 plus an i7 (Intel CPU Core i7-5930K 3.5 GHz (2011-3)). In order to test it, i run a MD simulation of a system containing ~90k atoms. These are the performances: 2 GPU’s (1 job): 34ns/day (each cards were working

Re: [gmx-users] Obtaining PMF for change in domain position

On 12/29/14 11:34 AM, Abhi Acharya wrote: On Mon, Dec 29, 2014 at 8:59 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/29/14 6:57 AM, Abhi Acharya wrote: Hello GROMACS Users, This is a problem I am facing for the first time. Kindly guide be to the best options. I have a protein which

Re: [gmx-users] charge distribution

On 12/29/14 3:32 PM, elham tazikeh wrote: Dear Justin thanks a lot for your response, your answers were very clear As you said,for building blocks i cant use of protein force field and i have to get from the literature(s) would you please recommend me some literature that i can use them?

[gmx-users] RDF does not reach 1 for bulk

Dear Gromacs users, I would like to know why the normalized RDF data from g_rdf does not reach 1 for bulk? As an alternative I tried using the raw data (i.e., by using the 'nonorm' flag) and normalized the values by dividing them by 'rho*volume of bin', which I believe is the standard method

[gmx-users] pdb information

Dear Justin i choosed *Cubic* box for amyloid beta peptide+Zn ion simulation for this reason, my *volume* is defined if i suppose that, Zn ion = 1 mol its concentration will be calculated my assumption is correct? cheers -- Gromacs Users mailing list * Please search the archive at