Re: [gmx-users] Weird structure after minimization (membrane proteinsimulation

2008-01-31 Thread Mark Abraham
[EMAIL PROTECTED] wrote: Dear Mark, & Chris, Thanks for your useful suggestions. Yes Mark define = -DFLEXIBLE is the only difference in both the cases. Actually in my previous post I have pasted only small section of tip4p.itp file,(sorry if it created unnecessary confusions/doubt). This time

Re: [gmx-users] Weird structure after minimization (membrane proteinsimulation

2008-01-31 Thread alokjain
Dear Mark, & Chris, Thanks for your useful suggestions. Yes Mark define = -DFLEXIBLE is the only difference in both the cases. Actually in my previous post I have pasted only small section of tip4p.itp file,(sorry if it created unnecessary confusions/doubt). This time I am pasting full tip4p.it

Re: [gmx-users] Weird structure after minimization (membrane proteinsimulation

2008-01-30 Thread Mark Abraham
[EMAIL PROTECTED] wrote: Dear Mark, Thanks a lot for your reply. Default was 1.6 angstrom and when I change gradually till 2.5 angstrom then structure looks similar to original structure. I have again checked in my top and mdp files for include statement. I have define = -DFLEXIBLE in my mdp

Re: [gmx-users] Weird structure after minimization (membrane proteinsimulation

2008-01-30 Thread alokjain
Sorry again, I just checked in case of TIP4P water molecules there is separate section [ constraints ] which is used if we do not use FLEXIBLE water. It does not uses SETTLE algorithm for constraining water molecules (correct me if I am wrong). Sorry for my previous mail. Regards, Alok > Dea

Re: [gmx-users] Weird structure after minimization (membrane proteinsimulation

2008-01-30 Thread alokjain
Dear Mark, Thanks a lot for your reply. Default was 1.6 angstrom and when I change gradually till 2.5 angstrom then structure looks similar to original structure. I have again checked in my top and mdp files for include statement. I have define = -DFLEXIBLE in my mdp file in my top file I have

Re: [gmx-users] Weird structure after minimization (membrane proteinsimulation

2008-01-29 Thread Mark Abraham
Alok wrote: Dear Mark & Chris, Thanks a lot for your help. As both of you suggested I have increased the tolerence limit of the bond (using VMD, as described by Chris), after increasing the Dynamic bond lenth, the structure looks fine. How long did you have to make the O-H bonds before it l

Re: [gmx-users] Weird structure after minimization (membrane proteinsimulation

2008-01-29 Thread Alok
ous help. Regards, Alok - Original Message - From: "Chris Neale" <[EMAIL PROTECTED]> To: Sent: Tuesday, January 29, 2008 1:29 AM Subject: [gmx-users] Weird structure after minimization (membrane proteinsimulation >Dear All, > >I am doing the simulation of POPE lipid