[gmx-users] OPLS parametrs for aminoxide

Hi all, I would like to know if the force field parameters (OPLS) exist for the amine oxide group (for eg as in trimethyl amine oxide (CH3)3-N-O ). In the OPLS parameter file in the gromacs tp directory, I could find only paramters for the nitro group (NO2) and NO3- ion. MD simulation of dimethyld

[gmx-users] OPLS parameters for amine oxide

Hi all, I would like to know if the force field parameters (OPLS) exist for the amine oxide group (for eg as in trimethyl amine oxide (CH3)3-N-O ). In the OPLS parameter file in the gromacs tp directory, I could find only paramters for the nitro group (NO2) and NO3- ion. MD simulation of dimethyld

Re: [gmx-users] g_hbond

India On Tue, Dec 13, 2011 at 10:12 AM, sulatha M. S wrote: > > > I did not get a warning here. I also have simulations (20ns) of >>> copolyacids where again it gave me negative life time. These runs are >>> well equilibrated with respect to energy and Rg of the polym

Re: [gmx-users] g_hbond

I did not get a warning here. I also have simulations (20ns) of >> copolyacids where again it gave me negative life time. These runs are >> well equilibrated with respect to energy and Rg of the polymers. The >> system is a 20 repeat unit chain in approx. 5500 water molecules. I have >> done simula

Re: [gmx-users] g_hbond

Dear David, Yes it is DGact. > The DGeq follows from the fraction of COOH that are not forming hydrogen > bonds, option -nhbdist. So, I need to use the equation (9) and (10) from your paper to calculate the equilibrium constant and free energy of H-bonding. >> Another question I have is, for a

[gmx-users] g_hbond

Dear gromacs users, I did a g_hbond -ac analysis on a 10 ns trajectory of a polycarboxylate in water. Following is the output I obtained for the polycarboxylate H-bondign with water ACF 36008/36008 Normalization for c(t) = 0.00709164 for gh(t) = 7.09124e-07 Hydrogen bond thermodynamics at T = 298

Re: [gmx-users] micelle clustering

are formed) Sulatha 2011/7/1 Mark Abraham > On 1/07/2011 3:35 PM, sulatha M. S wrote: > >> Hi Tsjerk, >> >> I installed gromacs myself. I put the modified gmx_trjconv.c code in the >> /src/tools subdirectory where the source code is located and tried the >> com

Re: [gmx-users] micelle clustering

:1611: warning: passing argument 1 of 'read_next_frame' makes integer from pointer without a cast gmx_trjconv.c:1611: warning: passing argument 2 of 'read_next_frame' from incompatible pointer type gmx_trjconv.c:1611: error: too many arguments to function 'read_next_frame&#x

[gmx-users] micelle clustering

Hi all, I have simulated a system of randomly dispersed surfactants in water using gromacs (4.0.7) for about 100 ns MD. Micelles are formed after around 40 ns. I am using a time step of 0.002 fs with xtc files written every 500 steps. For analyzing the micellar properties, I tried the commands gi

[gmx-users] Bromide ions in gromos forcefield

Hi, I plan to simulate a aqueous surfactant system with Bromide ions using the GROMOS 45a3 force field. As I understand Bromide ion has not been parametrized in GROMOS. I came across a paper by David van der Spoel, on "Encapsulation of Myoglobin in a Cetyl Trimethylammonium Bromide Micelle ..." u

Re: [gmx-users] OPLS and RB parameters in GROMACS

ce field. J. > Comput. Chem. 22:1340– > 1352. > > Best > Rainer > > On Feb 9, 2011, at 6:48 AM, sulatha M. S wrote: > > I looked at the the paper published in 1999, ( Jorgensen et al JACS, 121, > 20, 4831, 1999), the aliphatic torsional paramete

Re: [gmx-users] OPLS and RB parameters in GROMACS

= -4 * V4 Thanks Sulatha On Wed, Feb 9, 2011 at 11:31 AM, Mark Abraham wrote: > On 9/02/2011 4:48 PM, sulatha M. S wrote: > > I looked at the the paper published in 1999, ( Jorgensen et al JACS, 121, > 20, 4831, 1999), the aliphatic torsional parameters are the same as those >

Re: [gmx-users] OPLS and RB parameters in GROMACS

those originally published in 1996. > > Andrew > > On Tue, Feb 8, 2011 at 5:20 AM, sulatha M. S wrote: > >> Hi all, >> >> Hi >> >> >> >> I've converted the OPLS-AA torsional potential parameters for the >> >> alkane C-C-C-C (CT-CT-C

[gmx-users] OPLS and RB parameters in GROMACS

Hi all, Hi I've converted the OPLS-AA torsional potential parameters for the alkane C-C-C-C (CT-CT-CT-CT in the gromacs parameter file notation), C-C-C-H (CT-CT-CT-HC), and H-C-C-H (HC-CT-CT-HC) torsions from the OPLS format given in Jorgensen et al, JACS 118, 11225 (1996) to the Ryckaert-B

Re: [gmx-users] Potential Tables for user defined potentials

Thanks Justin, I have followed the How- tos/Polymers for creating rtp entries for polyacrylates/acids and have been able to run MD simulations successfully reproducing results from prior literature. Tabulated potentials section is also sure to help gmx-users. Thanks! Dr. M.S Sulatha IIT-Madras,

Re: [gmx-users] GROMOS96 parameters in itp file obtained from PRODRG

et the information on the details of itp file generated by PRODRG. Thanking you for any help, Sulatha > Mark Abraham wrote: > >> On 03/02/10 15:55, sulatha M. S wrote: >> >>> Dear gromas users, >>> I am new to gromacs and trying to run polyacrylate MD simulatio

[gmx-users] GROMOS96 parameters in itp file obtained from PRODRG

Dear gromas users, I am new to gromacs and trying to run polyacrylate MD simulation. I obtained an itp file using PRODRG (gromos 96 force-field parameters). When I compare with the same forcefield parameters in the gromacs/top directory, they are far too off. For eg. [ bonds ] ; ai aj fuc0