Re: [gmx-users] Question about DNA simulation

Hi, No there were no dummies, and without changing the masses in the non-bonded parameters file it would give infinite velocities. Regards Maik Goette wrote: Hi I never had to change masses in the nb.itp and I ran lots of simulations with the amber-Port...Are you sure, that you had no d

Re: [gmx-users] Question about DNA simulation

Hi I never had to change masses in the nb.itp and I ran lots of simulations with the amber-Port...Are you sure, that you had no dummies with mass zero or so? REgards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am F

Re: [gmx-users] Question about DNA simulation

Hi, Actually I think that although the .atp file seems to be used, the masses in the ffamberxxnb.itp file must be changed from the zero values to the correct ones: when I ran a simulation without changing them I got infinite velocities and which did nor happen when I changed the masses to

Re: [gmx-users] Question about DNA simulation

Maik Goette wrote: David I think, I should not contradict to one of the developers, but if your statement is true: 1. Where, in fact, are the masses coming from (the masses in the amberFF port can only be found in the atp, as far as I know)? 2. Why does GROMACS complain about missing atoms in

Re: [gmx-users] Question about DNA simulation

David I think, I should not contradict to one of the developers, but if your statement is true: 1. Where, in fact, are the masses coming from (the masses in the amberFF port can only be found in the atp, as far as I know)? 2. Why does GROMACS complain about missing atoms in the atp-file, if I

Re: [gmx-users] Question about DNA simulation

Maik Goette wrote: Because it is? The masses are defined in the .atp file. I dont't know how GROMACS handles the stuff, but that is sufficiantMaybe Eric was a bit lazy... Why do you care for that...? atp file is never used... Maik Goette, Dipl. Biol. Max Planck Institute for Biophysic

Re: [gmx-users] Question about DNA simulation

Because it is? The masses are defined in the .atp file. I dont't know how GROMACS handles the stuff, but that is sufficiantMaybe Eric was a bit lazy... Why do you care for that...? Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysic

[gmx-users] Question about DNA simulation

Hello, I have a question regarding DNA simulation. I have the amber99 package. Can anyone give me an explanation why all the masses in the ffamberXXnb.itpare 0? Thank you very much! Bo ___ gmx-users mailing listgmx-users@gromacs.org http://www.groma

[gmx-users] Question about DNA simulation

I am not sure if you read my previous reply here: http://www.gromacs.org/pipermail/gmx-users/2007-May/027730.html To be more explicit... you made a spelling mistake. "-D" is a flag and "FLEXIBLE" is what you are defining. You put an "E" between the two. Remove it. If that doesn't fix the proble

[gmx-users] Question about DNA simulation

Hi, As I mentioned in my last message, I also use pymol to visualize the molecule with water. I realize that the very top part of the DNA molecule is not surrounded by water molecules. I tried to varying the value for -d. Do you have any suggestions? Cheers~ Bo ___

[gmx-users] Question about DNA simulation

Hi everyone, I am still lost. For the DNA simulation that I am doing, I really don't know what is wrong. Is the em.mdp file (maybe temperature or other settings) inappropriate? Can you give me more specified explanation? Regards! Bo ___ gmx-users maili

[gmx-users] Question about DNA simulation, To: gmx-users@gromacs.org

Yes you need -DFLEXIBLE because you can't use constraints with em. Settle is a constraint for water. You problem is here: define =-DEFLEXIBLE -DEFLEXIBLE is not equal to -DFLEXIBLE ___ gmx-users mailing listgmx-users@gromacs.org http:

[gmx-users] Question about DNA simulation

Hi, When I do the DNA MD simulation. I use pdb2gmx, and the water model I used is spc.gro. I did the editconf and genbox. The following is my em.mdp file. define =-DEFLEXIBLE integrator =