Re: [gmx-users] Problem about Cgenff lone pairs

Thanks for your help. Best wishes, Shujie From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: Friday, February 8, 2019 11:58 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Problem about Cgenff lone pairs On 2/7/19

[gmx-users] The first coordination shell

HiI will appreciate if you tell me how can I calculate the first coordination shell of an ion?Thanks  -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] PBC conditions for Vacuum simulation

Hello gromacs users, I am trying to model a peptide in gas phase which requires proper conditions like: no PBC, no cut-offs for VanderWaals and electrostatics, coulomb type not PME. However, this increases computational time by N^2 for N number of atoms. Is there a way to mitigate this? Many

[gmx-users] Simulated Annealing

Dear Gromacs Users, How do we extend a simulated annealing? Thank you. Best Regards Shan Jayasinghe -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Fatal Lambda error

The lambda states are numbered from 0. You only have 21 different states in your mdp file. Therefore your init-lambda-state can range from 0 to 20. Cheers, Magnus Den fre 8 feb. 2019 23:08 skrev Angelina Malagodi < angelinamalag...@gmail.com>: > Sorry, if the attachments don't load, here are

[gmx-users] non-bond (Coulomb, van der Waals) interactions scaled down to 40% of their original value

HiHow can I scale down the non-bond (Coulomb, van der Waals) interactions to 40% of their original value in OPLS-AA forcefield?Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read