Re: [gmx-users] g_velacc. Reading frame 165000 time 825.000 Killed

Vitaly Chaban wrote: Hi, I calculate the diffusion constants via Green-Kubo relation for a system of 216 molecules (5 sites in each). The velocities are saved every 0.005 ps and the total trajectory is 1000 ps long. Then applying g_velacc -nonormalize -mol -n index.ndx -acflen 1001 The process s

Re: [gmx-users] how long simulation takes to get stable when constrains is none in mdp file?

wang kelvin wrote: hi: i am doing simulation of a system consists of 512 DMSO moleculers and 917 water moleculers. the whole system is running under 290K and 1bar ,and constraints = none; the simulation has taken 8000 ps ,but it seems not to get stable yet,because RMSD keeps rising. when i

Re: [gmx-users] g_velacc. Reading frame 165000 time 825.000 Killed

2008/8/5 David van der Spoel <[EMAIL PROTECTED]>: > Vitaly Chaban wrote: >> >> Hi, >> >> I calculate the diffusion constants via Green-Kubo relation for a >> system of 216 molecules (5 sites in each). The velocities are saved >> every 0.005 ps and the total trajectory is 1000 ps long. Then applying

[gmx-users] Define proper set of topology parameters for new molecule in different FF.

Dear gmx-users, I want to construct TOPOLOGY of many different molecules using different Force Fields (FF). If i want to describe , for example, METHYL ACETATE in OPLS-AA force field O Hc5 ||| C---O1C2Hc4 |

Re: [gmx-users] how long simulation takes to get stable when constrains is none in mdp file?

why RMSD? On Tue, Aug 5, 2008 at 9:19 AM, David van der Spoel <[EMAIL PROTECTED]> wrote: > wang kelvin wrote: >> >> hi: >> i am doing simulation of a system consists of 512 DMSO moleculers and >> 917 water moleculers. >> the whole system is running under 290K and 1bar ,and constraints = none; >

[gmx-users] table force-field

Hi Gromacs Users, In my simulation I have use very complicated potential, I obtained this potential from Boltzman Inversion of rdf, but when I trying run simulation I get error Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates.

Re: [gmx-users] table force-field

Alexandr Malafeev wrote: Hi Gromacs Users, In my simulation I have use very complicated potential, I obtained this potential from Boltzman Inversion of rdf, but when I trying run simulation I get error Range checking error: Explanation: During neighborsearching, we assign each particle to

Re: [gmx-users] how long simulation takes to get stable when constrains is none in mdp file?

Thanks for reply RMSD means root mean square deviation. I am researching DMSO properties during phase changes from nomal temperature to low tempreture. At first step,I want to produce fully equilibrant systems at different temperature. Of course ,there are many important parameters computed ,which

Re: [gmx-users] table force-field

2008/8/5 Justin A. Lemkul <[EMAIL PROTECTED]> > > > Alexandr Malafeev wrote: > >> Hi Gromacs Users, >> >> In my simulation I have use very complicated potential, I obtained this >> potential from Boltzman Inversion of rdf, but when I trying run simulation I >> get error >> >> Range checking error:

Re: [gmx-users] table force-field

Yes I done energy minimization, and mdrun output here: Steepest Descents converged to machine precision in 17 steps, but did not reach the requested Fmax < 10. Potential Energy = -1.6686725e+06 Maximum force = 2.4212272e+07 on atom 5 Norm of force = 3.4130568e+07 This would concern me a bit.

Re: [gmx-users] table force-field

2008/8/5 Justin A. Lemkul <[EMAIL PROTECTED]> > > Yes I done energy minimization, and mdrun output here: >> Steepest Descents converged to machine precision in 17 steps, >> but did not reach the requested Fmax < 10. >> Potential Energy = -1.6686725e+06 >> Maximum force = 2.4212272e+07 on atom 5 >

Re: [gmx-users] table force-field

Ok, Thank you very much, I will wait you reply. You got my reply :) Just to clarify - what I was saying was that "if I were you, I would check the configuration and parameters." I do not have the means (or the desire!) to do either for you. -Justin --

Re: [gmx-users] table force-field

2008/8/5 Justin A. Lemkul <[EMAIL PROTECTED]> > > > > >> Ok, Thank you very much, I will wait you reply. >> > > You got my reply :) Just to clarify - what I was saying was that "if I > were you, I would check the configuration and parameters." I do not have > the means (or the desire!) to do eit

[gmx-users] membrane with OPLS force field

Hello, I would like to simulate a membrane + protein system using the OPLS force field for both, the protein and the membrane. I have looked for a previous equilibrated membrane simulated using the OPLS force field, but I did not find it. Please, does anybody knows where I could find a membrane

Re: [gmx-users] membrane with OPLS force field

Rebeca García Fandiño wrote: Hello, I would like to simulate a membrane + protein system using the OPLS force field for both, the protein and the membrane. I have looked for a previous equilibrated membrane simulated using the OPLS force field, but I did not find it. Please, does anybody kno

[gmx-users] RE: Define proper set of topology parameters for new molecule in different FF.

>I want to construct TOPOLOGY of many different molecules using different >Force Fields (FF). > >If i want to describe , for example, METHYL ACETATE in OPLS-AA force field > > O Hc5 > ||| > C---O1C2Hc4 > |

[gmx-users] some questions about gmx_density.c

Hi, all Maybe since I am a newer with programming in C, I felt very difficult in reading codes of GROMACS. I want to know the arithmetic flow of gmx_density.c. I read many times but have no idea about it. Could anybody tell me the arithmetic flow of gmx_density.c? And where is the definitio

[gmx-users] RE: how long simulation takes to get stable when constrains is none in mdp file?

>why RMSD? > >On Tue, Aug 5, 2008 at 9:19 AM, David van der Spoel <[EMAIL PROTECTED]> wrote: > wang kelvin wrote: >> >> hi: >> i am doing simulation of a system consists of 512 DMSO moleculers and >> 917 water moleculers. >> the whole system is running under 290K and 1bar ,and constraints = none

[gmx-users] force feield paremeters for magnesium

hello GMX users I want to do simulation for a protein that has magnesium, how can I find force feield paremeters for magnesium and carboxyle oxygen ?. In God We Trust Hello Dear  Many thanks in advance for your help and your reply. Yours truly Karim Mahnam Institute of  Biochemistry  and Â

[gmx-users] membrane with OPLS force field

There is no such thing as an OPLS bilayer. The method that was specified to combine the opls-PROTEIN and berger-LIPIDS is currently the only way that one can do this combination exactly. What this means, is that if you simulate a bilayer using the files downloaded from Peter Tieleman's website

RE: [gmx-users] membrane with OPLS force field

Ok, thank you very much. However, with this combination I am not using all atoms for the lipds, if I am right and my intention was using all atoms both for the protein and the membrane. Thank you very much for your help. Best wishes, Rebeca García.> Date: Tue, 5 Aug 2008 09:44:17 -0400> From: [E

Re: [gmx-users] some questions about gmx_density.c

Hi, Perhaps gmx-devel is a better place for this mail. t_filenm does nothing with the algorithm flow. It's a struct to hold various input/output file names. The definition is found in some file under include/. Most analysis program follow a template as shown in share/template/template.c. What th

[gmx-users] membrane with OPLS force field

Sorry for my misunderstanding. You can not use standard OPLS parameters for lipids. Even if you go through the paramaterization process (see the gromace wiki and the original OPLS papers) then you are still stuck with the fact that standard acyl chain parameters fail when they get too long. I

[gmx-users] charge density

Hello All We have been trying to get the charge densities from the trajectory by using our in-house matlab code, which basically the same as a part of gmx_potential.c . z = x0[index[n][i]][axis]; if (z < 0) z += box[axis][axis]; if (z > box[axis][axi

Re: [gmx-users] force feield paremeters for magnesium

Mahnam wrote: hello GMX users I want to do simulation for a protein that has magnesium, how can I find force feield paremeters for magnesium and carboxyle oxygen ?. Ions are described in ions.itp, and carboxylate groups are a part of the description of the corresponding amino acid(s) fou

[gmx-users] RE: Define proper set of topology parameters for new molecule in different FF.

I want to construct TOPOLOGY of many different molecules using different Force Fields (FF). If i want to describe , for example, METHYL ACETATE in OPLS-AA force field O Hc5 || | C---O1C2Hc4 | | Hc3-- C1--Hc2

Re: [gmx-users] RE: Define proper set of topology parameters for new molecule in different FF.

Andrey Frolov wrote: I want to construct TOPOLOGY of many different molecules using different Force Fields (FF). If i want to describe , for example, METHYL ACETATE in OPLS-AA force field O Hc5 || | C---O1C2Hc4 |

[gmx-users] how to fix the COM of group in the pull.

Dear users: I want to know how to fix the com of the group in the pull or afm simulation,Please give some ideas. - 雅虎邮箱，您的终生邮箱！___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailm