subject:"\[gmx\-users\] gmx solvate problem"

Re: [gmx-users] gmx solvate problem

2017-11-08 Thread Smith, Micholas D.

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Alexandr Nasedkin Sent: Wednesday, November 08, 2017 9:40 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] gmx solvate problem Hi Golnaz, Try to increase default VdW radius scaling: option -scale in gmx solvate

Re: [gmx-users] gmx solvate problem

2017-11-08 Thread Alexandr Nasedkin

Hi Golnaz, Try to increase default VdW radius scaling: option -scale in gmx solvate. If there are large cavities in ICE you may have problem at water interface though. Best regards, Alexandr On 08/11/2017 15:04, G R wrote: Hi All, I’m simulating a box of tip4p ice. when I use the gmx

[gmx-users] gmx solvate problem

2017-11-08 Thread G R

Hi All, I’m simulating a box of tip4p ice. when I use the gmx solvate to fill the top and below part of the ice surface with solvent (the solvent is tip4p water), some of water molecules go to inside of the ice layers. I did not receive any errors, but the coordinate files became messy after salva