Re: [gmx-users] LINCS and number of nodes

2011-03-18 Thread Justin A. Lemkul
Moeed wrote: Hello Justin, Thanks for you reply. My late response is because I have been trying to resolve the problem. Dear experts, I am trying to build up a polymer in hexane system by increasing the density. After PR step, my NVT and NPT trailes failed.

Re: [gmx-users] LINCS and number of nodes

2011-03-18 Thread Moeed
Hello Justin, Thanks for you reply. My late response is because I have been trying to resolve the problem. Dear experts, >> >> I am trying to build up a polymer in hexane system by increasing the >> density. After PR step, my NVT and NPT trailes failed. Initially I used to >> get LINCS and 1-4 w

Re: [gmx-users] LINCS and number of nodes

2011-03-15 Thread Mark Abraham
On 16/03/11, Moeed wrote: > Dear experts, > > I am trying to build up a polymer in hexane system by increasing the density. > This seems to have been taking months. Why aren't you using genbox on your polymer starting configuration and an equilibrated box of hexane of the right density? M

Re: [gmx-users] LINCS and number of nodes

2011-03-15 Thread Justin A. Lemkul
Moeed wrote: Dear experts, I am trying to build up a polymer in hexane system by increasing the density. After PR step, my NVT and NPT trailes failed. Initially I used to get LINCS and 1-4 warnings (even for NVT) which were not because of flawed topology file. It turned out that simulations

[gmx-users] LINCS and number of nodes

2011-03-15 Thread Moeed
Dear experts, I am trying to build up a polymer in hexane system by increasing the density. After PR step, my NVT and NPT trailes failed. Initially I used to get LINCS and 1-4 warnings (even for NVT) which were not because of flawed topology file. It turned out that simulations crashed just becaus