Re: [gmx-users] Glycoproteion MD

Dear (sorry cant read chinese), You can find some OPLS or 53a6 Parameters on the web by doing extensive searches, mostly they are free, but hosted on varied individual lab web sites. That, or it may be easier to define some sets of bonds (angles, dihedrials, lengths charges, etc...from either

[gmx-users] Umbrella Sampling Pull code Problem

Dear Gromacs users, I have encountered a strange problem when trying to set up umbrella sampling simulations using gromacs 4.5.3. My system contains two groups with a COM distance of 1.95 nm (all distances measured by g_dist). Trying to set up the first US window, I use the following pull cod

?????? [gmx-users] Glycoproteion MD

Thanks for your help ,you can call me Guang.I come from China. -- -- ??: "lloyd riggs"; : 2012??8??31??(??) 7:25 ??: "Discussion list for GROMACS users"; : Re: [gmx-users] Glycoproteion MD Dear (sorry cant re

Re: [gmx-users] Glycoproteion MD

Hi, If you can't find parameters for glycoprotein's MD for charmm27, OPLS or Amber99 (and GROMOS is an alternative for you), we've been working on MD simulations with this class of biomolecules, using GROMOS96 43A1 force field, as described: Pol-Fachin, L.; Fernandes, C.L.; Verli, H.: GROMOS96

Re: [gmx-users] Umbrella Sampling Pull code Problem

I have met similar problem before. The distance calculated by g_dist is different from that calculated by grommp, especially when the actual distance between the two groups is very small. As the actual distance becomes larger, the difference of the distance from the two commands becomes smalle

Re: [gmx-users] Umbrella Sampling Pull code Problem

On Fri, Aug 31, 2012 at 1:45 PM, Steinbrecher, Thomas (IPC) wrote: > However, when I make the following two changes in my input file: > > pull_start = no > pull_init1 = 1.95 > > which should (?) amount to an equivalent setup, a very different trajectory > results in which the COM distan

[gmx-users] Turning off electrostatics between groups using custom tables?

Hi, I've been trying to turn off the electrostatic interaction between two groups (an ion-group and protein) by following the tutorial on custom table generation, but have seemed to have hit a road block. Looking at the structure of the sample 6-12 table provided in the topology directory, I const

[gmx-users] Re: Umbrella Sampling Pull code Problem

As Bogdan suggested this could be an issue with the sign of the distance. When you run grompp you get >Pull group natoms pbc atom distance at start reference at t=0 > 0 994 497 > 1 2 46347 1.224 1.950 which suggests your startin

Re: [gmx-users] Turning off electrostatics between groups using custom tables?

On 1/09/2012 1:14 AM, Smitty wrote: Hi, I've been trying to turn off the electrostatic interaction between two groups (an ion-group and protein) by following the tutorial on custom table generation, but have seemed to have hit a road block. Looking at the structure of the sample 6-12 table provi

[gmx-users] Re: Turning off electrostatics between groups using custom tables?

> While for the protein-protein or ion-group ion-group interactions I provide > just the standard 6-12 table. The problem comes that when I run using my > modified table, the system will run but gradually explodes. I note that > when > I look back at my output from grompp I find a warning concernin

Re: [gmx-users] Glycoproteion MD

Hi Guang, You can use the GLYCAM force field, which has parameters for carbohydrates and glycoproteins compatible with AMBER99. You can get the AMBER topology and structure files directly from their web interface, the "Online Glycoprotein Builder" ( http://glycam.ccrc.uga.edu/ccrc/gp/

Re: [gmx-users] Elastic network model

Hi all, I have built topology for elastic network as follows(the atoms which fall with in a distance less than 6 angtroms are bonded). [bonds] ;aiaj funct bo kb 2 1 1 3.80444752888 61.9 3 1 1 5.10184956658 61.9 3 2

Re: [gmx-users] Elastic network model

On Fri, Aug 31, 2012 at 8:42 PM, mohan maruthi sena wrote: > Hi all, > I have built topology for elastic network as follows(the > atoms which fall with in a distance less than 6 angtroms are bonded). > [bonds] > ;aiaj funct bo kb > 2 1 1 3.80

[gmx-users] Re: Force fields, is there a review article?

Thank you, Luca, for the link to the Ponder and Case review article. http://maxwell.uncc.edu/abaumket/phys6203_files/Reading/force-fields.pdf It is indeed the kind of article I have been seeking. > maybe one of the best thing to do is to test the FF vs experimental data > and check which one

Re: [gmx-users] Elastic network model

GROMACS uses nm as the unit of length, so this is 38 Angstroms, shouldn't be a problem. On 2012-08-31, at 2:23 PM, Bogdan Costescu wrote: > On Fri, Aug 31, 2012 at 8:42 PM, mohan maruthi sena > wrote: >> Hi all, >> I have built topology for elastic network as follows(the >> atoms

Re: [gmx-users] Elastic network model

On 1/09/2012 4:42 AM, mohan maruthi sena wrote: Hi all, I have built topology for elastic network as follows(the atoms which fall with in a distance less than 6 angtroms are bonded). [bonds] ;aiaj funct bo kb 2 1 1 3.80444752888 61.9 3

Re: [gmx-users] Re: Turning off electrostatics between groups using custom tables?

On 1/09/2012 2:50 AM, Smitty wrote: While for the protein-protein or ion-group ion-group interactions I provide just the standard 6-12 table. The problem comes that when I run using my modified table, the system will run but gradually explodes. I note that when I look back at my output from gromp

[gmx-users] Hydrogen bond breaking process

Can you tell me "how to predict the Hydrogen bond breaking process (For example Fe-CO hydrogen bond broken in Myoglobin at 100 ps) through MD simulation? Kind regards Rajiv -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the