Re: [gmx-users] Simulations in vacuo - energy increase

2011-04-30 Thread David van der Spoel
On 2011-04-30 14.17, Zoe Hall wrote: Gmx-users, I am trying to carry out a simulation of lysozyme in vacuo using the OPLS-AA forcefield. After energy minimisation, the protein is run for 10ps with position restraints and temperature coupling on. This is followed by the full production run of 10n

[gmx-users] Simulations in vacuo - energy increase

2011-04-30 Thread Zoe Hall
Gmx-users, I am trying to carry out a simulation of lysozyme in vacuo using the OPLS-AA forcefield. After energy minimisation, the protein is run for 10ps with position restraints and temperature coupling on. This is followed by the full production run of 10ns with temperature and pressure c

Re: [gmx-users] Simulations in vacuo

2011-01-12 Thread Erik Marklund
Zoe Hall skrev 2011-01-11 16.29: Hi gmx-users, I am trying to set up a simulation of a large protein /in vacuo/ using the OPLS-AA forcefield, with conditions based on Patriksson et. al (Biochemistry 2007, 46 p933). Basically after energy minimisation, the protein is run for 10ps in vacuum w

Re: [gmx-users] Simulations in vacuo

2011-01-11 Thread Mark Abraham
On 12/01/2011 2:29 AM, Zoe Hall wrote: Hi gmx-users, I am trying to set up a simulation of a large protein /in vacuo/ using the OPLS-AA forcefield, with conditions based on Patriksson et. al (Biochemistry 2007, 46 p933). Basically after energy minimisation, the protein is run for 10ps in va

[gmx-users] Simulations in vacuo

2011-01-11 Thread Zoe Hall
Hi gmx-users, I am trying to set up a simulation of a large protein in vacuo using the OPLS-AA forcefield, with conditions based on Patriksson et. al (Biochemistry 2007, 46 p933). Basically after energy minimisation, the protein is run for 10ps in vacuum with constant temperature at 300K. Thi