Re: [gmx-users] Simulation problem

2013-02-25 Thread Justin Lemkul
On 2/25/13 1:01 AM, Jernej Zidar wrote: Hi. I've been running some polymer simulations on our cluster and I'm getting this error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. What does this error

[gmx-users] Simulation problem

2013-02-24 Thread Jernej Zidar
Hi. I've been running some polymer simulations on our cluster and I'm getting this error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. What does this error mean? I imagine it is somehow related to the

RE: [gmx-users] Simulation problem with extended membrane system!

2006-09-07 Thread chris . neale
If you can't write a script, then do the minimization and equilibration with water frozen in the z dimension (freeze_groups = water; freeze_dim = n n y) or use constraints in the z dimension (posre.itp force constant 1000 along z and 0 along x and y). This will stop it from going into the membrane.

Re: [gmx-users] Simulation problem with extended membrane system!

2006-09-06 Thread liu xin
Hi ChrisThank you for your suggestions!These days I also tried anisotropic and semiisotropic for my simulation, but I still got the same result, so I wonder maybe there's something wrong with my initial structure, but it will take time to check it out. I'm trying to use the method you suggested, I

Re: [gmx-users] Simulation problem with extended membrane system!

2006-09-04 Thread chris . neale
It is unclear why your second method works for you. However, given that it does, just use genbox -cs spc216.gro -cp 183_system_that_worked.gro -box 9.2 9.2 8.3 and then use your own script to remove any spc waters that were put inside the membrane and modify the nubers in your topology file accordi

[gmx-users] Simulation problem with extended membrane system!

2006-09-01 Thread liu xin
Dear GMX-users:I met a problem when doing simulation with the membrane , here's what I've done so far:I download the dppc128.pdb file and dppc.top files from Dr. Tielman's website, equilibrated this dppc128 system for 10ns, I checked the final structure with VMD, everything seemed ok. Then I extend

Re: [gmx-users] Simulation problem

2006-02-27 Thread David van der Spoel
[EMAIL PROTECTED] wrote: Hi, I'm trying to EM a SDS bilayer. It seems everything is correct, however the mdrun exits with the following error: Getting Loaded... Reading file topol.tpr, VERSION 3.2.1 (single precision) Fatal error: calloc for ilist->iatoms (nelem=-1073805064, elsize=4, file tpx

[gmx-users] Simulation problem

2006-02-27 Thread stranger
Hi, I'm trying to EM a SDS bilayer. It seems everything is correct, however the mdrun exits with the following error: Getting Loaded... Reading file topol.tpr, VERSION 3.2.1 (single precision) Fatal error: calloc for ilist->iatoms (nelem=-1073805064, elsize=4, file tpxio.c, line 712): Cannot all