Re: [gmx-users] Problems with forcefield amber99 in Gromacs

> Hi, > I have a question regarding to using forcefield amber99 in Gromacs. > I have all the parameter files of amber99. > I am doing the MD of carbon nanotube with DNA. > I have changed the .pdb file of the DNA according to the instruction. > I generated the topology of DNA with identifying -water

[gmx-users] Problems with forcefield amber99 in Gromacs

Hi, I have a question regarding to using forcefield amber99 in Gromacs. I have all the parameter files of amber99. I am doing the MD of carbon nanotube with DNA. I have changed the .pdb file of the DNA according to the instruction. I generated the topology of DNA with identifying -water tip5p.gro.

Re: [gmx-users] Stuck ...

Hmm, yes, I do see your point. It was intended as a pun in reply to Stephanes comment to my request for a lot of information. But I do apologize in case people take offence. Maybe I should refrain from answering under fatigue... Tsjerk On 5/25/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: >

Re: [gmx-users] qm mm and charges in GMX!

Hi GMX'ers- specially Mark Abraham, At the GROMACS compiled with MOPAC 7.0, I tried to simulate my drug, using the QM/MM, at two *.itp files: (a) At the first I put the CHELPG charge fitting. (b) At the second itp file, I put zero charge since all the quantical or semi-empirical methods compu

[gmx-users] Stuck ...

If you could now send post your shoe size, your length and weight, and pictures of worthwhile sisters if you have any, we might be able to reinforce the incentive to help you :p These comments are totally unacceptable. I suppose it started out as a joke but it progresses into objectification o

Re: [gmx-users] free energy tutorial results

Please check your units: GROMACS uses kJ/mol, while the tutorial uses kcal/mol, if I remember correctly. So there's a factor 4.2 between those two. Ah, that's much better, by making the conversion I now get -2.168 which is quite a bit closer. Thanks for your help. I know I can be prone to som

Re: [gmx-users] Regarding downloading make_hole program

Dear Itamar, Thank you for your suggestion, one more request, is any tutorial available using this program. with regards, nagaraju ---

[gmx-users] Wiki online

Hi, since Mark spilled the beans, I might as well announce it officially: the GROMACS Wiki is online at http://wiki.gromacs.org. It is very much under construction still but there is already quite a bit of valuable stuff there. So please check it out. Cheers, -- David. __