Re: Re: [gmx-users] vacuum right but melt collapse

Tsjerk Wassenaar, thank you very much for you suggestion even if most of them have been manipulated. "Write out the energies at every step and check which of the energy contributions goes astray. This may give you a good clue to where you're mistake is. Also, run through the topology again, b

Re: [gmx-users] PME, epsilon_rf and dielectric constant calculation

> Dear Mark, > > I read the manual few times looking for a clue. The only thing I could > understand it that epsilon_rf is not taking inti account if I don't use > reaction field. 7.3.9 clearly says "epsilon_rf: (1) The relative dielectric constant of the reaction field. This is only used with rea

Re: [gmx-users] PME, epsilon_rf and dielectric constant calculation

Dear Mark, I read the manual few times looking for a clue. The only thing I could understand it that epsilon_rf is not taking inti account if I don't use reaction field. Best, Itamar. Mark Abraham wrote: Dear all, I wish to calculate the dielectric constant of small molecules liquids. In o

Re: [gmx-users] PME, epsilon_rf and dielectric constant calculation

> Dear all, > > I wish to calculate the dielectric constant of small molecules liquids. > In order to do so, I am simulating the system using PME, with epsilon_r > = 1. > > I have few questions: > 1. What is the meaning of epsilon_rf when I am using PME, if it > important, what it s

[gmx-users] PME, epsilon_rf and dielectric constant calculation

Dear all, I wish to calculate the dielectric constant of small molecules liquids. In order to do so, I am simulating the system using PME, with epsilon_r = 1. I have few questions: 1. What is the meaning of epsilon_rf when I am using PME, if it important, what it should be? 2.

Re: [gmx-users] genbox give coord file more waters than top file

> Dear gromacs guys > > Why would genbox put more water molecules in my .gro file than in my .top > file? I'm sure all I have to do is edit the number in my top file, but I > have not had this happen before, does anyone know of a reason that this > happens so I can fix my file? genbox doesn't rea

[gmx-users] genbox give coord file more waters than top file

Dear gromacs guys Why would genbox put more water molecules in my .gro file than in my .top file? I'm sure all I have to do is edit the number in my top file, but I have not had this happen before, does anyone know of a reason that this happens so I can fix my file? Will Welch ___

Re: [gmx-users] gmxcheck and trjconv

Hi Tsjerk, true i have to remember to start to count from 0 ... as usual :P thanks andrea Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) - Original Message - From: "Tsjerk Wassenaar" <[EM

[gmx-users] limitations in the umbrella sampling

Thanks a lot. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.

Re: [gmx-users] gmxcheck and trjconv

Hey Andrea, Also note that you have 70 FRAMES with 1 ps time step. That means, with the first frame at t=0, that you have a maximum time of (70-1)*1 ps = 69 ps in the output. Ciao! Tsjerk On 3/7/07, David van der Spoel <[EMAIL PROTECTED]> wrote: andrea spitaleri wrote: > Hi, > however in md0.

Re: [gmx-users] setup problem

Hi Merc, Probably, the .tpr file you used for trjconv -pbc nojump already had the ligand jumped. In that case, you will find all frames consistently having a shift between the ligand and the protein. Make sure you use a reference which has the ligand in place (the .pdb or .gro file you used to se

Re: Re: [gmx-users] vacuum right but melt collapse

Hi Ji Qing, Write out the energies at every step and check which of the energy contributions goes astray. This may give you a good clue to where you're mistake is. Also, run through the topology again, by hand, checking all bonds, angles, dihedrals, exclusion (implicit ones!), etc. Good luck, T

Re: [gmx-users] g_rdf

2007/3/7, marco cammarata <[EMAIL PROTECTED]>: Hi, I'm using g_rdf to calculate the RDF of a system. The "r range" ends at 3nm. r range ends at 3nm because (your box size)/2 is 3 nm I would like to change it to 100nm but it seems that there are no option for it. 100 nm? Are you sure?

Re: [gmx-users] g_rdf

marco cammarata wrote: Hi, I'm using g_rdf to calculate the RDF of a system. The "r range" ends at 3nm. I would like to change it to 100nm but it seems that there are no option for it. Can you help me ? thanks, marco The CVS version has an option to turn off the periodic boundary conditions. T

RE: [gmx-users] limitations in the umbrella sampling

From: Seungho Choe <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] limitations in the umbrella sampling Date: Tue, 06 Mar 2007 17:33:38 -0500 Dear all, In the manual, it says : If a group contains part of a molecule of which the

[gmx-users] g_rdf

Hi, I'm using g_rdf to calculate the RDF of a system. The "r range" ends at 3nm. I would like to change it to 100nm but it seems that there are no option for it. Can you help me ? thanks, marco -- Marco Cammarata, Post-Doc European Synchrotron Radiation Facility Material Science Group 6, rue Ju

Re: [gmx-users] gmxcheck and trjconv

andrea spitaleri wrote: Hi, however in md0.log the right time is reported (69 and not 70) and David van der Spoel wrote: andrea spitaleri wrote: Hi all, silly question. I have checked a trr with gmxcheck and I get this output below: Item#frames Timestep (ps) Step701 Ti

Re: [gmx-users] gmxcheck and trjconv

Hi, however in md0.log the right time is reported (69 and not 70) and David van der Spoel wrote: > andrea spitaleri wrote: >> Hi all, >> silly question. I have checked a trr with gmxcheck and I get this >> output below: >> Item#frames Timestep (ps) >> Step701 >> Time

Re: [gmx-users] gmxcheck and trjconv

Hi nope they are both finished. I have also checked the edr files and the time does not correspond to the time found in the respectively trr files. Those MD are carried out in a supercomputer (SARA in Amsterdam) and they were killed by the queue system. Probably as you said a buffer problem ...

Re: [gmx-users] positive system total-energy

Qiao Baofu wrote: Hi David, Thanks for your reply! It is a pure ionic liquid system. I compared this energy result with that of another system, found that the term of "Coul.-recip." is very smaller (-4664.24) than another system's result (- 56014.1). All other terms of the energy are in t

Re: [gmx-users] gmxcheck and trjconv

andrea spitaleri wrote: Hi all, silly question. I have checked a trr with gmxcheck and I get this output below: Item#frames Timestep (ps) Step701 Time701 Lambda 701 Coords 701 Velocities 243 Forces 0 Box

[gmx-users] gmxcheck and trjconv

Hi all, silly question. I have checked a trr with gmxcheck and I get this output below: Item#frames Timestep (ps) Step701 Time701 Lambda 701 Coords 701 Velocities 243 Forces 0 Box 701 however if th

Re: [gmx-users] Fwd: Atom index (1) in settles out of bounds (1-0)

> Sorry, > I digged through the post-list of old user-questions and found the same > problem occuring. > the answer to the question was written by David v.d.Spoel and was: > "the position in the top file where the spc.itp was included is wrong". > > In my top file this include statement is at the e

[gmx-users] Atom index (1) in settles out of bounds (1-0)

Dear users, I have a question regarding a simulation (using the amber ports) of DNA covalently bound to a protein. First of all I made an entry in the specbond.dat and the bond was correctly build between the a P of the DNA and a Tyr of the protein. After that I started grompp and got the followi

[gmx-users] Fwd: Atom index (1) in settles out of bounds (1-0)

Sorry, I digged through the post-list of old user-questions and found the same problem occuring. the answer to the question was written by David v.d.Spoel and was: "the position in the top file where the spc.itp was included is wrong". In my top file this include statement is at the end of the sc

Re: [gmx-users] Which force-field for DNA-protein complex ?

I'm currently using AMBER03 for a DNA-protein complex. A little bit of struggle and extra examination of topologies and such was needed when setting up the system, but nothing too daunting. /Erik 7 mar 2007 kl. 01.12 skrev mathieu coincon: I searched the database in order to choose which f

Re: [gmx-users] positive system total-energy

Hi David, Thanks for your reply! It is a pure ionic liquid system. I compared this energy result with that of another system, found that the term of "Coul.-recip." is very smaller (- 4664.24) than another system's result (-56014.1). All other terms of the energy are in the same order of magni

Re: [gmx-users] setup problem

thank you for your suggestions. actually i tried all -pbc options, but neither did help. but i think i found the solution in an old posting from ka feenstra. there he writes that due to efficiency (iirc) at least one atom of each part of the system has to be in the rectangular waterbox. therefor