Re: [gmx-users] H2 topology

2010-02-04 Thread Mark Abraham
13...@bioinfo.sastra.edu> Date: Wednesday, February 3, 2010 21:48 Subject: Re: [gmx-users] H2 topology To: Discussion list for GROMACS users Dear David, Thanks for your reply. From your reply, I get the impression that the bond length of my hydrogen molecule gets adjusted duing minimizatio

Re: [gmx-users] H2 topology

2010-02-04 Thread 011013021-Jyotsna
is message was transferred with a trial version of CommuniGate(r) Pro* - Original Message - From: 011013021-Jyotsna <011013...@bioinfo.sastra.edu> Date: Wednesday, February 3, 2010 21:48 Subject: Re: [gmx-users] H2 topology To: Discussion list for GROMACS users Dear Da

Re: [gmx-users] H2 topology

2010-02-03 Thread Mark Abraham
- Original Message - From: 011013021-Jyotsna <011013...@bioinfo.sastra.edu> Date: Wednesday, February 3, 2010 21:48 Subject: Re: [gmx-users] H2 topology To: Discussion list for GROMACS users > > Dear David, > > Thanks for your reply. From your reply, I get the >

Re: [gmx-users] H2 topology

2010-02-03 Thread David van der Spoel
On 2/3/10 10:18 AM, 011013021-Jyotsna wrote: Dear David, Thanks for your reply. From your reply, I get the impression that the bond length of my hydrogen molecule gets adjusted duing minimization of the whole system ( protien+water+ inserted hydrogen molecule). But the issue impending is the in

Re: [gmx-users] H2 topology

2010-02-03 Thread 011013021-Jyotsna
Dear David, Thanks for your reply. From your reply, I get the impression that the bond length of my hydrogen molecule gets adjusted duing minimization of the whole system ( protien+water+ inserted hydrogen molecule). But the issue impending is the insertion of the hydrogen molecule itself

Re: [gmx-users] H2 topology

2010-02-03 Thread David van der Spoel
On 2/3/10 7:52 AM, 011013021-Jyotsna wrote: Dear Justin , Thank you very much for your help. To create a linear H2 molecule with a dummy atom in the center is proving to be quite a difficult task. Hence , I created a pdb file of CO2 using Cerius(2) , and replaced the atoms in the pdb file with

[gmx-users] H2 topology

2010-02-03 Thread 011013021-Jyotsna
Dear Justin , Thank you very much for your help. To create a linear H2 molecule with a dummy atom in the center is proving to be quite a difficult task. Hence , I created a pdb file of CO2 using Cerius(2) , and replaced the atoms in the pdb file with 2 H atoms and a dummy atom.(since CO2 is a

Re: [gmx-users] H2 topology

2010-02-02 Thread Justin A. Lemkul
r own sake, please cultivate that habit :-) Mark Thank you, Jyotsna Re: [gmx-users] H2 topology David van der Spoel Mon, 01 Feb 2010 04:02:06 -0800 On 2/1/10 10:57 AM, 011013021-Jyotsna wrote: Dear all, I want to run a simulation for an enzyme. It demands me to incorporate a Molecular hyd

Re: [gmx-users] H2 topology

2010-02-02 Thread Thomas Piggot
the tables in section 5.7.1. Science in general and computational science in particular is very exacting. For your own sake, please cultivate that habit :-) Mark Thank you, Jyotsna Re: [gmx-users] H2 topology David van der Spoel Mon, 01 Feb 2010 04:02:06 -0800 On 2/1/10 10:57 AM, 011013021

Re: [gmx-users] H2 topology

2010-02-02 Thread Justin A. Lemkul
computational science in particular is very exacting. For your own sake, please cultivate that habit :-) Mark Thank you, Jyotsna Re: [gmx-users] H2 topology David van der Spoel Mon, 01 Feb 2010 04:02:06 -0800 On 2/1/10 10:57 AM, 011013021-Jyotsna wrote: Dear all, I want to run a simulation for an

Re: [gmx-users] H2 topology

2010-02-02 Thread 011013021-Jyotsna
. For your own sake, please cultivate that habit :-) Mark Thank you, Jyotsna Re: [gmx-users] H2 topology David van der Spoel Mon, 01 Feb 2010 04:02:06 -0800 On 2/1/10 10:57 AM, 011013021-Jyotsna wrote: Dear all, I want to run a simulation for an enzyme. It demands me to incorporate a

Re: [gmx-users] H2 topology

2010-02-01 Thread Mark Abraham
the tables in section 5.7.1. Science in general and computational science in particular is very exacting. For your own sake, please cultivate that habit :-) Mark Thank you, Jyotsna Re: [gmx-users] H2 topology David van der Spoel Mon, 01 Feb 2010 04:02:06 -0800 On 2/1/10 10:57 AM, 011013021

[gmx-users] H2 topology

2010-02-01 Thread 011013021-Jyotsna
is between the two Hydrogen atoms of btween the dummy atom and each of the Hydrogen atoms in either side, in which case the total distance becomes 1.4 A. When i mention the bond distance in the topology file , should it be placed under Bond or constraint? Thank you, Jyotsna Re: [gmx-users

Re: [gmx-users] H2 topology

2010-02-01 Thread David van der Spoel
On 2/1/10 10:57 AM, 011013021-Jyotsna wrote: Dear all, I want to run a simulation for an enzyme. It demands me to incorporate a Molecular hydrogen Topology with a dummy atom in between in the simulation in order to study the path of hydrogen in it.The problem is , the topology file I built induc

[gmx-users] H2 topology

2010-02-01 Thread 011013021-Jyotsna
Dear all, I want to run a simulation for an enzyme. It demands me to incorporate a Molecular hydrogen Topology with a dummy atom in between in the simulation in order to study the path of hydrogen in it.The problem is , the topology file I built induces many errors when i come to the energy