[gmx-users] construct lipid bilayer from single lipid (fwd)

-- Forwarded message -- Date: Sat, 11 Aug 2007 20:12:28 +0800 From: Q733 <[EMAIL PROTECTED]> To: David van der Spoel <[EMAIL PROTECTED]> Subject: construct lipid bilayer from single lipid Dear Professor Spoel: I have read your steps on how to construct a lipid bilayer from a singl

RE: [gmx-users] a basic question

I had exactly this problem. The reason was I've edited mdp file at Windows. Sounds silly, I know, but just do your editing for mdp at Linux, it solved the problem for me. Yulia Einav Ph.D. From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Q

Re: [gmx-users] Suggestion needed for new workstation

Am Freitag, 10. August 2007 schrieb Erik Lindahl: > >> RAM size shouldn't be an issue, except if you're simulating huge > >> systems. > > > > RAM is essential for some analysis tools and if you want to do ab > > initio > > calculations. Ok, i was mainly concerned about doing longer simulations, y

[gmx-users] Fatal error: more tahn

Dear all, When I use distance constrains(NMR), there happens such errors: Fatal error: More than 8 graph edges per atom (atom 1) I have more than 8 constrains on atom 1. What's reason? Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological U

Re: [Bulk] 回复:Re: [Bulk] [gmx-users] a qu estion about potential energy

hi, my suggestion is still the previous one, get g_energy to plot a Energy vs. time for you so you will know where this average value comes from. Regards, Yang Ye On 8/12/2007 10:34 AM, [EMAIL PROTECTED] wrote: > > Dear Yany Ye > > Thank you for your help. I am indeed a new man as you guess. I a

[gmx-users] construct lipid bilayer from a single lipid

Yesterday I tried to construct a lipid bilayer through a single lipid. The process is like this: 1. editconf -f lipid.pdb -princ -c -box 0.8 0.8 3.0 -o lipid.gro 2. genconf -f lipid.gro -nbox 4 4 1 -o box.gro 3. modified vanderwals radii in the vanradii.dat in the top folder ,changed the C value

[gmx-users] Difference between pbc=full and pbc=xyz

Hi, Everyone, I'm simulating a infinite polymer and so I set "pbc=full". After I shift some atoms by box size, the energy minimization just broke down. The error message is just like the following: Fatal error: ci = -2147483648 should be in 0 .. 1457. Everything is OK before the shift. Then