Re: [gmx-users] error during minimization

2012-11-27 Thread Justin Lemkul
On 11/27/12 4:31 AM, Shine A wrote: Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. But during minimization (after shrinking), getting error like this. Fatal error: Invalid line in system_shrink26.gro for atom 8703: 6.4140 6.44350 6.59650.why this er

Re: [gmx-users] error during minimization

2012-11-27 Thread Venkat Reddy
Probably..there is a problem in spacing at the bottom of your gro file. The line mentioning the vectors should be like this eg:, 5012OBC49 47 1.088 1.094 2.775 0.0 0.0 0.0 On Tue, Nov 27, 2012 at 3:01 PM, Shine A wrote: > Sir, > >I am studying the dynamics o

[gmx-users] error during minimization

2012-11-27 Thread Shine A
Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. But during minimization (after shrinking), getting error like this. Fatal error: Invalid line in system_shrink26.gro for atom 8703: 6.4140 6.44350 6.59650.why this error?plz give me a solution to overcome it. -

Re: [gmx-users] error during minimization

2012-10-11 Thread Justin Lemkul
On 10/11/12 10:27 AM, Shine A wrote: Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. But during minimization getting error like this.. There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 18.5346 nm

[gmx-users] error during minimization

2012-10-11 Thread Shine A
Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. But during minimization getting error like this.. There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 18.5346 nm Change the number of nodes or mdrun opti

Re: [gmx-users] Error during minimization

2010-01-05 Thread Mark Abraham
nishap.pa...@utoronto.ca wrote: I have a question regarding the simulations that I am running. I tried creating a pdb file with one methane and water molecules, but the system keeps showing 'bad contact' error when I run the minimization step and I don't understand what I am doing wrong. Thi

[gmx-users] Error during minimization

2010-01-05 Thread Chris Neale
Hi Nisha, you say "And it runs minimization with bad contact errors", but I don't see any indication of that error message here. Is it perhaps that your EM exits early and then your MD throws an error? In any event, please post complete error information as output by gromacs. Chris. -- origi

[gmx-users] Error during minimization

2010-01-05 Thread nishap . patel
I have a question regarding the simulations that I am running. I tried creating a pdb file with one methane and water molecules, but the system keeps showing 'bad contact' error when I run the minimization step and I don't understand what I am doing wrong. This is my methane file : TITLE