Re: [gmx-users] rvdw, rlist and rcoulomb for Amber03

On 8/25/13 12:01 AM, Rajat Desikan wrote: Hi Justin, In a recent post (http://gromacs.5086.x6.nabble.com/VDW-Cut-off-vs-Switch-with-CHARMM-force-field-td5010695.html;cid=1377399737789-944) you commented that: "Unless you can demonstrate that your changes in cutoffs do not produce artifacts or

[gmx-users] rvdw, rlist and rcoulomb for Amber03

Hi Justin, In a recent post (http://gromacs.5086.x6.nabble.com/VDW-Cut-off-vs-Switch-with-CHARMM-force-field-td5010695.html;cid=1377399737789-944) you commented that: "Unless you can demonstrate that your changes in cutoffs do not produce artifacts or lead to other inaccuracies using robust test s

Re: [gmx-users] rvdw and dispersion correction for amber99sb

In the original paper [Comparison of multiple Amber force fields and development of improved protein backbone parameters], 0.8 nm was used; but I did find recent papers using 1.0 nm for rvdw. And I myself used 1.4 nm, all without obvious abnormality. On Mon, Aug 20, 2012 at 10:13 PM, Mark Abraham

Re: [gmx-users] rvdw and dispersion correction for amber99sb

On 21/08/2012 2:30 PM, Yun Shi wrote: Hello all, I am simulating protein-ligand complex with amber99sb force field in TIP3P water. What would be a reasonable value rvdw? I saw someone uses 1.0, and I did not find any abnormality when using 1.4 nm for rvdw, but where can I find the right referen

[gmx-users] rvdw and dispersion correction for amber99sb

Hello all, I am simulating protein-ligand complex with amber99sb force field in TIP3P water. What would be a reasonable value rvdw? I saw someone uses 1.0, and I did not find any abnormality when using 1.4 nm for rvdw, but where can I find the right reference? And is this force field parameteriz

Re: [gmx-users] rvdw and DispCorr

On Fri, 2012-05-11 at 10:23 +0200, Bernhard Knapp wrote: > Dear gromacs users > > In a recent paper I found the following protocol of a gromacs simulation: > > "All simulations were performed with the GROMACS 4.0 [12] compiled in > single-precision mode at a constant temperature of 277 K in a p

[gmx-users] rvdw and DispCorr

Dear gromacs users In a recent paper I found the following protocol of a gromacs simulation: "All simulations were performed with the GROMACS 4.0 [12] compiled in single-precision mode at a constant temperature of 277 K in a periodic box with an edge length of approximately 8.2 nm and the defaul

Re: [gmx-users] rvdw vs cut-off / different types of non bonded interactions

Dear Sir, I'm absolutely aware that gromacs uses nm for distance. The values should be 0.556 and 0.89. I used them only for reference purposes and I hope that this didn't cause any misanderstanding so as to point me to the manual. If this is the case of not understanding my questions, I deeply app

Re: [gmx-users] rvdw vs cut-off / different types of non bonded interactions

On Wed, 12 Dec 2007, Claus Valka wrote: Dear Sir, I would try to be more precise. example1 mdp file: rlist = (greater or equal to rvdw) vdw-type = Switch rvdw-switch=5.56 rvdw=8.9 are you aware that gromacs usues nm for distance? you can find the functional form of the shift/switch functi

Re: [gmx-users] rvdw vs cut-off / different types of non bonded interactions

Dear Sir, I would try to be more precise. example1 mdp file: rlist = (greater or equal to rvdw) vdw-type = Switch rvdw-switch=5.56 rvdw=8.9 Between the value 5.56 and 8.9 gromacs uses cubic spline? example2 mdp file: rlist=5.56 vdw-type = Cut-off rvdw-switch=0 (this value here should be irrele

Re: [gmx-users] rvdw vs cut-off / different types of non bonded interactions

Claus Valka wrote: Hello, 3rd question: Which is the difference between the S(hort)R(ange) LJ and LJ 1-4? For me the short range interactions are the 1-4LJ, yet it seems that this is not the case. GROMACS uses twin-range cutoffs (see manual), so LJ-SR is inside the shorter cutoff, and LJ-L

[gmx-users] rvdw vs cut-off / different types of non bonded interactions

Hello, I have searched thoroughly the manual and the gmx list, yet with no avail. I'm trying to understand how I will be able to implement to gromacs my system which is complicated as far as the non bonded interactions are concerned. My system comprises three different types of atoms. The LJ int

Re: [gmx-users] rvdw

Oops..., indeed, Gromos was parameterized for use with 1.4 nm :SShould also have checked my sources first. Scuziscuziscuzi...TsjerkOn 6/21/06, Isabella Daidone <[EMAIL PROTECTED]> wrote: Thanks Tsjerk,but what about the following gromacs page:http://www.gromacs.org/blogcategory/page_4.htmland the

Re: [gmx-users] rvdw

Thanks Tsjerk, but what about the following gromacs page: http://www.gromacs.org/blogcategory/page_4.html and the following article of van Gunsteren "J Comp Chem, 1998, 19:535" which suggests the use of 1.4 nm? Thanks Isabella On Wed, 21 Jun 2006, Tsjerk Wassenaar wrote: Hi Isabella, The Gro

Re: [gmx-users] rvdw

Hi Isabella,The Gromos force fields were parameterized for use with a rvdw cutoff of 0.9. Other cutoffs may introduce artefacts.Ciao!TsjerkOn 6/21/06, Isabella Daidone <[EMAIL PROTECTED]> wrote: Sorry, but I'm a little bit confused about what rvdw to use forsimulations of proteins in solution with

[gmx-users] rvdw

I see that with version 3.3 is now possible to use rvdw>rcoulomb. So I guess rvdw=1.4 should be used. What about simulations done with version 3.1.4, where rvdw=0.9 nm was used? How to justify that? Thanks Isabella ___ gmx-users mailing listgmx-u

[gmx-users] rvdw

Sorry, but I'm a little bit confused about what rvdw to use for simulations of proteins in solution with gromos96 force field while using pme for coulomb interactions. In the gromacs 3.3 manual I still read (with pme): rcoulomb=rlist=rvdw=0.9 nm Then, I found in the discussion list (+ the paper