RE: [gmx-users] Viscosity in PE

Thanx! Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden -Original Message- From: [EMAIL PROTECTED] on behalf of Berk Hess Sent: Fri 9/8/2006 8:34 AM To: gmx-users@gromacs.org Subject: Re: [gmx-users] Viscosi

Re: [gmx-users] Viscosity in PE

From: David van der Spoel <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] Viscosity in PE Date: Thu, 07 Sep 2006 19:36:34 +0200 Esther Caballero-Manrique wrote: You can calculate it from the velocity autocorrelat

Re: [gmx-users] Re: Simulation problem with extended membrane system!

Hi ChrisThank you for your note!According to your suggestion, I did a energy minimization and then a MDS with "freezegrps=SOL, freezedim=N, N, Y", the rest of the system were simulated with no constraint. This time I use semiisotropic pressure coupling with tau_p=5. The system will be equilibrated

Re: [gmx-users] how to exclude some atoms from coulomb interaction calculation?

Cherry Y. Yates wrote: Dear all, I did a massive MD simulation of nanostructure. In my calculation, over 80% atoms have zero charge and the main CPU time is devoted to Coulomb interaction. I wonder if anyone knows how to exclude these neutral atoms from Coublomb interaction so that a lot of C

[gmx-users] why the mdrun stop

  hello ,everyone   I have two problems: (1)my model is compost of 36 long chain of CH3(CH2)14COOH  ,and use the frocefiled of ffgmx, but the mdrun can only going to the 2th step,and the some chains change large (2)can this program do the nanotribology of   monolayer? thanks advanced! wait for you

Re: [gmx-users] why the mdrun stop

zzhwise1 wrote: hello ,everyone I have two problems: (1)my model is compost of 36 long chain of CH3(CH2)14COOH ,and use the frocefiled of ffgmx, but the mdrun can only going to the 2th step,and the some chains change large (2)can this program do the nanotribology of monolayer? thanks ad

Re: [gmx-users] why the mdrun stop

Shalom, You did not mention if you did energy minimization or other preliminary steps before your MD. If not, this might solve the problem. Best, Itamar. Quoting zzhwise1 <[EMAIL PROTECTED]>: > > hello ,everyone > I have two problems: > (1)my model is compost of 36 long chain of CH3(CH2)14COO

[gmx-users] genion causing atom to be in multiple T-Coupling groups

Dear Users, I'm trying to neutralize my system adding 3 Cl ions with genion and when running grompp again with the new generated .gro file I get this error: Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1) which is the last water atom (total in system 33003) and groups 15 and 1

[gmx-users] Splitting one run

Hi there, I heard that there's an unofficial script to split one run in several small ones. Anyone of you remembers the topic so that I can search for it? Regards Martin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org

[Fwd: Re: Re: [gmx-users] why the mdrun stop]

Original Message Subject:Re: Re: [gmx-users] why the mdrun stop Date: Fri, 8 Sep 2006 21:58:02 +0800 (CST) From: zzhwise1 <[EMAIL PROTECTED]> To: david van der spoel <[EMAIL PROTECTED]> References: <[EMAIL PROTECTED]> <[EMAIL PROTECTED]> I try 3 long chain

[gmx-users] Re: Simulation problem with extended membrane system!

>According to your suggestion, I did a energy minimization and then a MDS >with "freezegrps=SOL, freezedim=N, N, Y", the rest of the system were >simulated with no constraint. This time I use semiisotropic pressure >coupling with tau_p=5. The system will be equilibrated with water >constrained for

[gmx-users] TFE .gro files

Title: TFE .gro files Hello all, Does anyone have TFE (trifluoroethanol) .gro files that they might be willing to share?  Or, barring that, can anyone tell me how to create a solvent .gro file? Much thanks, Jeff Copps ___

[gmx-users] Coulomb 1-4 interactions

Hi gmx-users:   I am running a comparison between AMBER and Gromacs for a AOT system. First I created the AMBER force field and then transformed it to Gromacs force field. I did 1 step of MD respectively in AMBER and Gromacs with the same configuration. All the energy terms including bond, angle, d

Re: [gmx-users] Coulomb 1-4 interactions

Justin, What is your fudgeQQ value in ffamberXX.itp? This value (I think the default is 0.8333) should be the reciprocal of scaling factor used in Amber's input file (I think the default is 1.200). Check amber's manual specific parameter name for it. (I don't remember off my head right now.) Be

Re: [gmx-users] Coulomb 1-4 interactions

> Hi gmx-users: > > I am running a comparison between AMBER and Gromacs for a AOT system. > First > I created the AMBER force field and then transformed it to Gromacs force > field. There are existing ports that you can find in the User Contributions section of the GROMACS webpage. Comparing yours

[gmx-users] can the GMX model the monolayer frict ion ?

  hello everyone     I want to know whether GMX can simulate the LB monolayer  or selfassemble monolayer on base ?if can not ,could advise one to me?   thanks!      买 这 些 让 女 友 很 兴 奋 ( 图 ) 真 会 过 日 子 ! 一 个 月 收 入 5800 漂 亮 MM 的 感 性 生 活 ( 组 图 ) ___

Re: [gmx-users] can the GMX model the monolayer frict ion ?

> > hello everyone > I want to know whether GMX can simulate the LB monolayer or > selfassemble monolayer on base ?if can not ,could advise one to me? > thanks! Yes it is mathematically capable of doing that. You would know this, and a whole lot more, if you read the GROMACS webpage thoroug

[gmx-users] LINCS warning

Dear all, I have a query, 1. Are two trajectories comparable if each one of them has been run in a different version of gromacs? Eg, v3.2 and v3.3. Thanks in advance, Regards, Raghu ** Y. M. Ragothaman, Research Scholar, Centre for Computational Biology and Bio