Re: [gmx-users] Shutting down in Windows2000

Thanks Mark for your reply, I run MD for 100 (2ns) at dt = 0.002. In both occasion, shutdown happened during mid night at around 7800 steps. I could not fix the problem by looking at log file as it does not contain any information regarding this. Is it possible that the gromacs could influenc

Re: [gmx-users] Shutting down in Windows2000

raja wrote: Dear Gmxions, While I run MD (Gromacs 3.3.1) in cygwin under windows2000 for 2ns, it shuts off automaticaly after 2days . It happened in two different machine installed windows2000 professional. Any previous experience by any of this sort ? Not that I've hear

[gmx-users] Shutting down in Windows2000

Dear Gmxions, While I run MD (Gromacs 3.3.1) in cygwin under windows2000 for 2ns, it shuts off automaticaly after 2days . It happened in two different machine installed windows2000 professional. Any previous experience by any of this sort ? But it works perfect for windowsX

[gmx-users] grompp error:Invalid order for directive defaults

Dear GMX users, I'd like to study the interaction between carbon nanotube and a polymer chain. I have made cnt.itp for the nanotube and poly.itp. Both itp files contains force field parameters (such as [ defaults ], [ atomtypes], [ bondtypes ]), in this way, I don't need to include any force field

Re: [gmx-users] grompp warning: atom names don't match - with respect to solvent

You should remove water atoms from topology fileArneh Babakhani <[EMAIL PROTECTED]> wrote: Hi All, thanks for the replies. I figured out the problem. I had fragmented water molecules in my initial structure. After deleting those fragments, the warning went away. Thanks!Diana Rodriguez Ortiz wrote:

Re: [gmx-users] grompp warning: atom names don't match - with respect to solvent

Hi All, thanks for the replies. I figured out the problem. I had fragmented water molecules in my initial structure. After deleting those fragments, the warning went away. Thanks! Diana Rodriguez Ortiz wrote: check that the atom names match in your pdb and topology and that they match to the p

[gmx-users] Adding hydrogen

Hi, Dear Gromacs Users, Seems pdb2gmx just can add hydrogen to the main chain, not side chain (one can check the tutor demo file). I wonder whether it is not necessary to add hydrogen on the side chain in Gromacs or one has to add the side chain hydrogen by other software. I appreciate very much if