[gmx-users] Lennard-Jones potential for protons

Dear Gromacs Users, Hi, I'm trying to simulate a system with a free proton included. However, I wasn't able to find Lennard-Jones parameters for free protons in charmm, amber, and opls ff. On the other hand, there are parameters for other cations such as Na, K, etc. Is there any reason why par

Re: [gmx-users] Lennard-Jones potential for protons

One does not have a free proton in a condensed phase simulation, which is what all those force fields target. And even if you do, a classical-mechanics description of it will probably be poor at best. Mark On Wed, Jul 3, 2013 at 9:35 AM, Jong Wha Lee wrote: > Dear Gromacs Users, > > > > Hi, I'm

[gmx-users] Testing the performance of

Hello, I want some inputs on observed performance of protein-in-water simulations run on a single server with 2 Intel Xeon E5-2660 processors. Each processor has 8C/16T, so total 16C/32T. My system is composed of 1643 beta-microglobulin atoms and 24699 water atoms. I ran several 500ps simulation

Re: [gmx-users] Testing the performance of

On Wed, Jul 3, 2013 at 10:17 AM, Richa Singh wrote: > Hello, > > I want some inputs on observed performance of protein-in-water > simulations run on a single server with 2 Intel Xeon E5-2660 > processors. Each processor has 8C/16T, so total 16C/32T. My system is > composed of 1643 beta-microglobul

[gmx-users] how to deal with LINCS warnings despite prolonged stabilization of the system?

Dear all, I'm writing again because I really need to understand what more can I do on my systems that are still dealing with LINCS warnings. I minimized further the systems (from emtol 500 to emtol 100) and the final potential energies and max force were nearly identical to those I obtained wh

Re: [gmx-users] how to deal with LINCS warnings despite prolonged stabilization of the system?

This kind of instability boils down to "if the starting configuration and model physics are capable of running a stable simulation, you're being too rough with it" - as http://www.gromacs.org/Documentation/Terminology/Blowing_Up says using different words. Each time one changes the ensemble, that'

Re: [gmx-users] Lennard-Jones potential for protons

I am also not aware of the force field parameters for hydrated/solvated proton, but maybe I am just wrong here. An attempt to describe proton with Newtonian dynamics will unlikely give you anything similar to reality. Lennard-Jones parameters play no role here, by the way, some force fields assign

Re: Re: [gmx-users] how to deal with LINCS warnings despite prolonged stabilization of the system?

Dear Mark, thank you very much for your answer. I'll try to do what you suggest, but what makes me crazy is that when the simulation stops, I have no indication at all about what happens to the system (or at least, I don't know how to search for these indications). I'd like to understand what

Re: Re: [gmx-users] how to deal with LINCS warnings despite prolonged stabilization of the system?

On Wed, Jul 3, 2013 at 1:23 PM, Anna Marabotti wrote: > Dear Mark, > thank you very much for your answer. I'll try to do what you suggest, but > what makes me crazy is that when the simulation stops, I have no indication > at all about what happens to the system (or at least, I don't know how to >

[gmx-users] Atomtype OWT3 not found during EM step

Dear all, I am a new user of GOMACS. My system contains Polymer and Water. I used gromos53a6 force field and spc water model, it ran nicely. But now I want to use TIP3P water model with the same force field (gromos53a6), in that case, I am getting a error message from the 'grompp' during energy

[gmx-users] Atomtype OWT3 not found during EM step

Dear all, I am a new user of GOMACS. My system contains Polymer and Water. I used gromos53a6 force field and spc water model, it ran nicely. But now I want to use TIP3P water model with the same force field (gromos53a6), in that case, I am getting a error message from the 'grompp' during energy m

Re: [gmx-users] Atomtype OWT3 not found during EM step

I would guess the new atom type should be in the ITP file. And of course, you are expected to define bonded and nonbonded terms for all applicable pairs, triples... of atoms. Good luck. Dr. Vitaly V. Chaban On Wed, Jul 3, 2013 at 6:41 PM, Juganta K. Roy wrote: > Dear all, > > I am a new user

Re: [gmx-users] Atomtype OWT3 not found during EM step

On 7/3/13 12:46 PM, juganta wrote: Dear all, I am a new user of GOMACS. My system contains Polymer and Water. I used gromos53a6 force field and spc water model, it ran nicely. But now I want to use TIP3P water model with the same force field (gromos53a6), in that case, I am getting a error me

[gmx-users] unwrap trajectory file using -pbc nojump

Dear all, I want to remove PBC effects for my system and calculate the diffusion coefficient. I am using Gromacs 4.5.4. My system is a 15 nm cubic box with 376 polymer chains each with 28 beads. The simulation time is about 2000 ns. However, when I use the command trjconv_mpi -f all.xtc -s

Re: [gmx-users] unwrap trajectory file using -pbc nojump

Hi Yutian Yang, I don't think it's because of the size of the system. Can you run trjconv without -pbc nojump? And did you check the trajectory with gmxcheck? Does the output file exceed a maximum file size limit? Hope it helps, Tsjerk On Wed, Jul 3, 2013 at 9:22 PM, Yutian Yang wrote: > De

[gmx-users] Re: Re: Lennard-Jones potential for protons

Thank you Mark and Vitaly. I understand that simulation of protons in the solution phase is unphysical. Though I haven't mentioned beforehand, I'm actually trying to simulate noncovalent interaction between a proton and a carbonyl oxygen in the gas phase. Could you give me any ideas how I may s

[gmx-users] g_velacc

Dear all I have calculated the diffusion coefficient using command g_msd and I want to calculate diffusion coefficient using command g_velacc. I am confused with some terms. 1>I have looked the manual page of g_velacc and i found the statement "the time interval between data collection points is

Re: [gmx-users] g_velacc

On 2013-07-04 05:38, Ishwor wrote: Dear all I have calculated the diffusion coefficient using command g_msd and I want to calculate diffusion coefficient using command g_velacc. I am confused with some terms. 1>I have looked the manual page of g_velacc and i found the statement "the time interva

[gmx-users] Re: g_velacc

I have really tried to calculate diffusion coefficient using both commands but i cant find the comparable results. i have my *.mdp file as ;PREPROCESSING parameters tinit = 0 integrator = md dt =.002 nsteps = 1 nstcomm = 1 ;O