Re: [gmx-users] Charmm Sugars/carbohydrates

All of the Charmm force field parameters may be found on Alex MacKerell's website: http://mackerell.umaryland.edu/ CHARMM_ff_params.html. Converting from Charmm units and potential form to Gromacs is straightforward. Andrew On Dec 7, 2011, at 12:59 PM, Michael McGovern wrote: Hi everyone.

Re: [gmx-users] Non zero total charge

I believe your problem is that you do not understand scientific notation. 5.70e+01 = 57. Cl- has a charge of -1. Need I say more. On Thu, Sep 1, 2011 at 11:46 AM, Munishika Kalia wrote: > Hi, > > The genion command i used is > genion -s genion.tpr -o ago_water_ions.gro -nn 6 > > I used this t

Re: [gmx-users] Lennard Jones interactions

, Andrew Paluch wrote: The LJ interaction is 0. But you're asking about a bond. 1-2 interactions are typically modeled with a harmonic potential. This is most definitely not zero. On Jun 10, 2011, at 2:54 PM, Nilesh Dhumal wrote: If eplilon of hydrogen atom is zero then the lennard

Re: [gmx-users] Lennard Jones interactions

The LJ interaction is 0. But you're asking about a bond. 1-2 interactions are typically modeled with a harmonic potential. This is most definitely not zero. On Jun 10, 2011, at 2:54 PM, Nilesh Dhumal wrote: If eplilon of hydrogen atom is zero then the lennard jones interaction of OH bond

Re: [gmx-users] Lennard Jones interactions

You can calculate that by hand on a calculator in a few seconds. There is no need to use Gromacs. On Jun 10, 2011, at 2:27 PM, Nilesh Dhumal wrote: Hello, How can I calculate Lennard Jones interaction for two selected atoms with a specific distance? I am using Gromacs 4.0.7 version. Tha

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

There is no error. The alkane dihedral parameters were updated in 1999, and differ from 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 (C

Re: [gmx-users] TIP3P water box

If you get this to work, you may still have problems as SPC and TIP3P have different geometries. A box of 216 waters is pretty easy to equilibrate; you could have this done for TIP3P in no time at all. On Apr 16, 2010, at 4:46 AM, kecy...@sina.com wrote: Hello,I want to use spc216.gro an

Re: [gmx-users] New ion parameters and OPLS-AA

Read the manual. You can explicitly declare all of your cross terms rather than using the same mixing rule for all terms. You can easily write a script to modify your input files accordingly, Andrew On Tue, Dec 15, 2009 at 4:06 PM, Reza Salari wrote: > Hi All, > > Recently there has been a ne

Re: [gmx-users] Problems with calculating Cv and Cp

interested in, you may have better luck with a water model other than TIP3P. Hope this helps, Andrew ___ _______ Andrew Paluch Department of Chemical and Biomolecular Engineering University of Notre Dame du Lac

[gmx-users] g_current

Does anyone know of a reference (besides the manual) for the calculations performed by g_current? Thank you, Andrew ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at h

Re: [gmx-users] 1-4 interactions

You can either specify this explicitly or use the fudge LJ and fudge q headers in your topology file. See the manual for details. On Sep 26, 2009, at 1:51 AM, Vitaly V. Chaban wrote: Hi, Is it possible in gromacs to make 1-4 interaction energy reduced as compared to the intermolecular inter

[gmx-users] Buckingham Potential

run-time flags that I should be using? Thank you, Andrew ___ ___ Andrew Paluch Department of Chemical and Biomolecular Engineering University of Notre Dame du Lac apal...@nd.edu

[gmx-users] Gromacs in Parallel

To whom this may concern, I am receiving the following errors when attempting to run Gromacs in parallel: Making 1D domain decomposition 4 x 1 x 1 p2_21562: p4_error: Timeout in establishing connection to remote process: 0 p2_21562: (302.964844) net_send: could not write to fd=5, errno = 32 wh

[gmx-users] FudgeLJ

To whom this may concern, Is it possible to use FudgeLJ to scale 1-4 interactions when using a Buckingham Potential? Also, are long range corrections implemented for the Buckingham Potential? Thank you, Andrew ___ gmx-users mailing listgmx-