Re: [gmx-users] Restraining water molecule

2013-03-21 Thread Justin Lemkul
On 3/21/13 8:10 AM, neeru sharma wrote: Message: 1 Date: Thu, 21 Mar 2013 07:05:44 -0400 From: Justin Lemkul Subject: Re: [gmx-users] Restraining water molecule To: Discussion list for GROMACS users Message-ID: <514ae988.4050...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1;

[gmx-users] Restraining water molecule

2013-03-21 Thread neeru sharma
> > Message: 1 > Date: Thu, 21 Mar 2013 07:05:44 -0400 > From: Justin Lemkul > Subject: Re: [gmx-users] Restraining water molecule > To: Discussion list for GROMACS users > Message-ID: <514ae988.4050...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=

Re: [gmx-users] Restraining water molecule

2013-03-21 Thread Justin Lemkul
On 3/21/13 4:29 AM, neeru sharma wrote: Message: 6 Date: Wed, 20 Mar 2013 09:04:05 -0400 From: Justin Lemkul Subject: Re: [gmx-users] Restraining water molecule To: Discussion list for GROMACS users Message-ID: < caduqwc5+fotchpmi0pqeexcnpkbtqa-yb0px1p889gy3jza...@mail.gmail.

Re: [gmx-users] Restraining water molecule

2013-03-20 Thread Justin Lemkul
On Wed, Mar 20, 2013 at 8:57 AM, neeru sharma wrote: > Dear gromacs users, > > I am simulating a system of Protein-ion-GTP with One Water molecule. I want > to restrain this system (along with this water molecule) for minimization > and equilibration. > > Everytime I run this by specifying the .it

[gmx-users] Restraining water molecule

2013-03-20 Thread neeru sharma
Dear gromacs users, I am simulating a system of Protein-ion-GTP with One Water molecule. I want to restrain this system (along with this water molecule) for minimization and equilibration. Everytime I run this by specifying the .itp files, it gives the error of misplacement as follows: *"This pr

Re: [gmx-users] Restraining water

2010-12-05 Thread Oliver Grant
I would use grep and cut to take the atom numbers of the residues I want to restrain and direct them into an index file with [res_sol] at the top. Then use genrestr to generate restraints for these atoms using the -n option. Then conditionally include this restraint file (.itp file) in my topology

Re: [gmx-users] Restraining water

2010-12-02 Thread David Rodríguez
2010/12/2 Mark Abraham > On 2/12/2010 12:51 PM, Guido Polles wrote: > >> Hi, >> I know it looks a little bit strange, but i was trying to restrain >> just some water in my system. >> Now, if i put something like >> [ position_restraints ] >> ; i funct fcxfcyfcz >>11

Re: [gmx-users] Restraining water

2010-12-01 Thread Mark Abraham
On 2/12/2010 12:51 PM, Guido Polles wrote: Hi, I know it looks a little bit strange, but i was trying to restrain just some water in my system. Now, if i put something like [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 I put restrai

[gmx-users] Restraining water

2010-12-01 Thread Guido Polles
Hi, I know it looks a little bit strange, but i was trying to restrain just some water in my system. Now, if i put something like [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 I put restraints on all the molecules. I thought about a tu