Re: [gmx-users] Constraining a part of the system

2013-09-17 Thread HANNIBAL LECTER
Does anyone have proper parameters for CNTs ? I have been trying to perform Simulations with finite CNTs. However, none of the parameters so far (obtained from literature) seem to give the output temperatures equal to set temperatures. I have been looked into my input files time and again, but I c

Re: [gmx-users] Constraining a part of the system

2013-09-17 Thread Dr. Vitaly Chaban
the smart way is to constrain everything at once in MDP... Dr. Vitaly V. Chaban On Tue, Sep 17, 2013 at 10:50 PM, HANNIBAL LECTER wrote: > Is there a smart way of writing the constraint sections in the topology > file other than entering the values manually ? > > > On Tue, Sep 17, 2013 at 10:10

Re: [gmx-users] Constraining a part of the system

2013-09-17 Thread HANNIBAL LECTER
Is there a smart way of writing the constraint sections in the topology file other than entering the values manually ? On Tue, Sep 17, 2013 at 10:10 AM, rahul seth wrote: > Thanks > > > On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul wrote: > > > > > > > On 9/17/13 10:00 AM, HANNIBAL LECTER wro

Re: [gmx-users] Constraining a part of the system

2013-09-17 Thread HANNIBAL LECTER
Yes. That is the way to go about it. I was hoping for a more lazy approach... Thanks anyways. On Tue, Sep 17, 2013 at 5:07 PM, Justin Lemkul wrote: > > > On 9/17/13 4:50 PM, HANNIBAL LECTER wrote: > >> Is there a smart way of writing the constraint sections in the topology >> file other than en

Re: [gmx-users] Constraining a part of the system

2013-09-17 Thread HANNIBAL LECTER
@Vitaly. Yes you are right. However, I noticed that if I do not constraint the bonds in my CNT my simulations run fine. It is indeed surprising to me but I do not have much experience with simulating CNTs and if not constraining the bonds seem to get things done, I think it is a viable option. But

Re: [gmx-users] Constraining a part of the system

2013-09-17 Thread Justin Lemkul
On 9/17/13 4:50 PM, HANNIBAL LECTER wrote: Is there a smart way of writing the constraint sections in the topology file other than entering the values manually ? Write a script that parses the [bonds] directive of the post-processed topology (output by grompp -pp) and write the relevant fie

Re: [gmx-users] Constraining a part of the system

2013-09-17 Thread Justin Lemkul
On 9/17/13 10:00 AM, HANNIBAL LECTER wrote: Is there a way to constraint bonds of a part of the system while keeping the other part flexible? For example for a simulation with two proteins, I would like to constraint the bonds of one and would like to keep the other flexible. I would prefer to

[gmx-users] Constraining a part of the system

2013-09-17 Thread HANNIBAL LECTER
Is there a way to constraint bonds of a part of the system while keeping the other part flexible? For example for a simulation with two proteins, I would like to constraint the bonds of one and would like to keep the other flexible. I would prefer to use LINCS to constraint the system -- gmx-user

Re: [gmx-users] Constraining a part of the system

2013-09-17 Thread rahul seth
Thanks On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul wrote: > > > On 9/17/13 10:00 AM, HANNIBAL LECTER wrote: > >> Is there a way to constraint bonds of a part of the system while keeping >> the other part flexible? For example for a simulation with two proteins, I >> would like to constraint