Hi all,I am trying to perform explicit molecular dynamics simulations on a transmembrane protein. I performed minimization for 10,000 steps and then performed equilibration in three steps: 1) water equilibration with lipid constrained2) water equilibration with protein and lipid constrained3) full dynamic equlibrationEverything worked fine so far, except the PBC was a little reduced in a few decimal points, so I moved on to the production run of system for 50ns at 300K temperature. However, after a few ns, the shape and size of water box started to change. It would be highly appreciated if somebody could guide me to understand the problem.
Bets regards,Mahrukh ImtiazCOMSATS Institute of Information TechnologyIslamabad
On Thursday, November 24, 2016 11:02 AM, Mahrukh Imtiaz <mahrukhimtiaz92.yahoo.com> wrote:
Hi all,I am trying to perform explicit molecular dynamics simulations on a transmembrane protein. I performed minimization for 10,000 steps and then performed equilibration in three steps: 1) water equilibration with lipid constrained2) water equilibration with protein and lipid constrained3) full dynamic equlibrationEverything worked fine so far, except the PBC was a little reduced in a few decimal points, so I moved on to the production run of system for 50ns at 300K temperature. However, after a few ns, the shape and size of water box started to change. I am attaching images of before and after the production run. Moreover, I am also attaching my input file. It would be highly appreciated if somebody could guide me to understand the problem.
Bets regards,Mahrukh ImtiazCOMSATS Institute of Information TechnologyIslamabad
On Wednesday, November 23, 2016 3:34 PM, Mahrukh Imtiaz <mahrukhimtiaz92.yahoo.com> wrote:
Hi all,I am trying to perform explicit molecular dynamics simulations on a transmembrane protein. I performed minimization for 10,000 steps and then performed equilibration in three steps: 1) water equilibration with lipid constrained2) water equilibration with protein and lipid constrained3) full dynamic equlibrationEverything worked fine so far, except the PBC was a little reduced in a few decimal points, so I moved on to the production run of system for 50ns at 300K temperature. However, after a few ns, the shape and size of water box started to change. I am attaching images of before and after the production run. Moreover, I am also attaching my input file. It would be highly appreciated if somebody could guide me to understand the problem.
Bets regards,Mahrukh ImtiazCOMSATS Institute of Information TechnologyIslamabad
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Received on Wed Nov 23 2016 - 22:30:02 PST
