Re: [gmx-users] Warning: 1-4 interaction

2011-03-11 Thread Moeed
Dear experts, I have been trying to do NVT on a system (a single polyethylene chain in 110 hexane) in the past few days but still no success. For some reason simulations are taking much longer than before. A run that used to complete in a few hours is taking several weeks. I am wondering if there

Re: [gmx-users] Warning: 1-4 interaction

2011-03-05 Thread Justin A. Lemkul
Moeed wrote: Hello Justin, I just scanned through the manual and also looked into the list to learn about the significance of reciprocal part to realize your statement. I did not find much about the fact that how I can judge if fourierspacing is the cause of the crash (I mean relevance betw

Re: [gmx-users] Warning: 1-4 interaction

2011-03-05 Thread Moeed
Hello Justin, I just scanned through the manual and also looked into the list to learn about the significance of reciprocal part to realize your statement. I did not find much about the fact that how I can judge if fourierspacing is the cause of the crash (I mean relevance between fourierspacing a

Re: [gmx-users] Warning: 1-4 interaction

2011-03-05 Thread Mark Abraham
On 06/03/11, Moeed wrote: > Hi everyone, > > My attempt to conduct a NPT failed although everything seemed to be going > well. Topology is OK and I am just curious why system is blowing up all of a > sudden towards the end of simulation. I should mention that by changing > fourierspacing fr

Re: [gmx-users] Warning: 1-4 interaction

2011-03-05 Thread Justin A. Lemkul
Moeed wrote: Hi everyone, My attempt to conduct a NPT failed although everything seemed to be going well. Topology is OK and I am just curious why system is blowing up all of a sudden towards the end of simulation. I should mention that by changing fourierspacing from 0.12 to 0.3 everything

[gmx-users] Warning: 1-4 interaction

2011-03-05 Thread Moeed
Hi everyone, My attempt to conduct a NPT failed although everything seemed to be going well. Topology is OK and I am just curious why system is blowing up all of a sudden towards the end of simulation. I should mention that by changing fourierspacing from 0.12 to 0.3 everything works fine till the

[gmx-users] Warning: 1-4 interaction

2007-04-12 Thread Joern Lenz
dear gromacs guys, i have the following problem: i linked the phosphate atom of a DNA to the phenolic-hydroxyl group of a proteins tyrosine by defining a line in the specbond.dat file. the distance before linking these atoms was about 4.2 angstroms. my intention now was first to minimize the link