Re: [gmx-users] remd ... is it exchanging?

Carsten Baldauf wrote: dear all// i am trying to run remd simulations on a 16 residue peptide using 16 replicas in a temperature range from 275 to 419 kelvin. i follow the method described here: Seibert, M., Patriksson, A., Hess, B., van der Spoel, D. Reproducible polypeptide folding and struct

Re: [gmx-users] remd ... is it exchanging?

Carsten Baldauf wrote: ok, i got it wrong ... i see now my problem ... i am using an extremely big box ... the length of my fully extended peptide is about 5.6 nm i will try a box with an image distance of 5.7 nm. this should more or less resemble the status of your input, am i right? In fact

Re: [gmx-users] remd ... is it exchanging?

ok, i got it wrong ... i see now my problem ... i am using an extremely big box ... the length of my fully extended peptide is about 5.6 nm i will try a box with an image distance of 5.7 nm. this should more or less resemble the status of your input, am i right? thanks for the help// carsten

Re: [gmx-users] remd ... is it exchanging?

Carsten Baldauf wrote: dear david// i never used pymol ... in your paper you write you solvated using pymol. is it a plugin or or a standard feature? can you give me a hint how to do it? It doesn't write that... We used pymol (pymol.sf.net) to generate the starting structure of our peptide.

Re: [gmx-users] remd ... is it exchanging?

dear david// i never used pymol ... in your paper you write you solvated using pymol. is it a plugin or or a standard feature? can you give me a hint how to do it? thanks// carsten David van der Spoel wrote: Carsten Baldauf wrote: dear all// i am trying to run remd simulations on a 16 resid

Re: [gmx-users] remd ... is it exchanging?

Carsten Baldauf wrote: dear all// i am trying to run remd simulations on a 16 residue peptide using 16 replicas in a temperature range from 275 to 419 kelvin. i follow the method described here: Seibert, M., Patriksson, A., Hess, B., van der Spoel, D. Reproducible polypeptide folding and struct