[gmx-users] Is Generalized Born implicit solvent model faster than explicit solvent model?

Hi everyone, I did two reMD simulations with GB implicit solvent and TIP3P solvent using Gromacs4.5.5 respectively (1 cpu per replica for both of them). My results show that implicit solvent model is not faster than explicit solvent model. I'm confused why the implict solvent model is so slow? Or

Re: [gmx-users] Three molecules in single topol.top file

Dear Jang, it seems that some of angles in your topology file are not defined in bonded interaction. you can check angle constructed by atom 13 2 in your topology file. On 8/31/16, Chang Woon Jang wrote: > Dear Mark Abraham, > > I am a little confused about the

[gmx-users] QM/MM simulations (Mark Abraham) (Groenhof, Gerrit)

Is is true that the gau script available at http://wwwuser.gwdg.de/~ ggroenh/qmmm.html only works with gromacs versions < 5? -- Clinton King Graduate Student Chemistry Department Brigham Young University > > >5. Re: QM/MM simulations (Mark Abraham) (Groenhof, Gerrit) > > Hi, > > Unless there

Re: [gmx-users] Three molecules in single topol.top file

Dear Mark Abraham, I am a little confused about the meaning of "you have not taught grompp how to handle" (especially *taught*) because I have topology file, conf.gro, nonbonded and bonded force fields, grompp.mdp, index file. Do I need to do something else in order to specify the

Re: [gmx-users] Three molecules in single topol.top file

Dear Nikhil Maroli, I think that the error comes from the incorrect format of topology file. Therefore, I would like to create correct topology file for three molecules. The system I used is a customized coarse-grained system to which I mapped the atomistic system. Therefore, I need to modify

Re: [gmx-users] Three molecules in single topol.top file

Hi, There's no need to use separate itp files.the include mechanism just pastes it back in. The actual error message shows you have an interaction that you have not taught grompp how to handle. Investigate that. Mark On Wed, 31 Aug 2016 18:12 Nikhil Maroli wrote: > It is

Re: [gmx-users] Three molecules in single topol.top file

It is impossible to make any comments without knowing the simulation details. I hope it will help , if not provide the full details http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ gmx-tutorials/complex/02_topology.html -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Three molecules in single topol.top file

Dear Sako Mirzaie, Thank you for your response. Do you mean that there is no way to include topologies in a single topol.top, and I need to separate them into three pieces of itp files? Best regards, Changwoon Jang On Wed, Aug 31, 2016 at 11:57 AM, SAKO MIRZAIE

Re: [gmx-users] Three molecules in single topol.top file

Dear Nikhil Maroli, Thank you for your link. However, I think that the link is just the example for a single type of molecule. My has three different types of molecules combined into a single topology file (topol.top). In the previous, I have three (TDM, J230, JMT) moleculetypes. I have

Re: [gmx-users] Three molecules in single topol.top file

because it is incorrect format. the topology can be produced by pdb2gmx automatically. for several molecules, you could include them as itp file format. On Wed, Aug 31, 2016 at 8:05 PM, Nikhil Maroli wrote: > http://manual.gromacs.org/online/top.html > > And what is the

Re: [gmx-users] Three molecules in single topol.top file

http://manual.gromacs.org/online/top.html And what is the error? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe

Re: [gmx-users] topology build.

1. Google 2. Tutorials 3. Manual -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit

[gmx-users] Three molecules in single topol.top file

Dear Gromacs Users, I have a single topol.top file containing three molecules. Does this format is correct because the simulation keeps failing? Thank you. [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 1 no 0.0

[gmx-users] Force-Field for Ketals

Hi, I want to model a linear compound that has a ketal component. While building the OPLSAA topology (.itp) file for this molecule I ran into not having the C-C-C angle parameterized in -O-(CH3)2C-O-. I have spent some time looking for a different force field that may have this entire molecule,

Re: [gmx-users] Does Gromacs support MVAPICH2 & MVAPICH2-GDR?

Hi, Yes. http://manual.gromacs.org/documentation/2016/install-guide/index.html#mpi-support Mark On Wed, Aug 31, 2016 at 4:12 PM DeChang Li wrote: > Dear all, > > I want to use gromacs with MPI in Infiniband network & GPU. It seems that > MVAPICH2 performs better with

[gmx-users] Does Gromacs support MVAPICH2 & MVAPICH2-GDR?

Dear all, I want to use gromacs with MPI in Infiniband network & GPU. It seems that MVAPICH2 performs better with Infiniband network. Does gromacs support MVAPICH2? Best, Dechang Li, Ph.D = *Biomechanics and Biomaterials Laboratory* *Department of Applied

[gmx-users] topology build.

Thanks for your reply. From your instruction I have been build the topology. During energy minimization step error occur as *Ryckaert-Bell. types.* What the parameters should i missing..?? Hope you reply... -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] pulling the wall

As far as I know, that is not possible in GROMACS. You can set the wall to accelerate in a certain direction using the mdp options. This would give a constant pressure since it would result in constant force on the wall (roughly) but not constant velocity. Evan L. On Aug 31, 2016 3:04 AM, "pari

[gmx-users] pulling the wall

Dear all, How I connect a harmonic spring to a wall for pulling wall with a certain velocity? Thanks in advance, Pari -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] ATB parametrization of small molecule

Hello everyone I want to simulate a protein ligand docked complex using GROMOS96 43a1 force field. I have prepared the ligand topology using ATB server. However, I want to know how can I validate the results of ATB when no experimental or computational data is available for small molecule. I have