[gmx-users] Solvent_box

Hi, Sorry for the inconvenience caused. The output from the script suggests that the pdb file is written. However when i open the pdb file the solvent box is not created in full. Since i could not provide the structure on the mailing list it was a bit difficult for the other person to comprehend

Re: [gmx-users] Solvent_box

Hi Prasenjit, Okay, this one's more clear in regards your objective (should've read my mail in chronological order). Your problem is basically the handling of PBC itself. The trick is to give a center with the option -center, and to apply this to the first atom of the solute. Note that gromacs al

[gmx-users] Solvent_box

Hi users, To answer Mark's question about reading section 3.2. Yes I have.I wish to conduct an SMD study.I want to place my protein system at one end of the longest side of triclinic shell and then pull parallel to the longest side. Yang I have used both pymol and VMD for visualization Tsjerk

Re: [gmx-users] Solvent_box

Hi Prasenjit, In addition to the previous comments, note that the default triclinic box has -angles set to 90 90 90. If you want to have something other than rectangular, you need to set the angles explicitly. Also, you issue -d 0.9 and -box 20 10 10. I'm not sure what will happen, but obviously

Re: [gmx-users] Solvent_box

Which visualization software you have used? On 7/12/2007 1:47 PM, pkmukher wrote: Hi, I am trying to build a triclinic solvent box around two.pdb using the following commands editconf -bt triclinic -f two.pdb -o three.pdb -d 0.9 -box 20 10 10 genbox -cp three.pdb -cs spc216.gro -o four.pdb -

Re: [gmx-users] Solvent_box

pkmukher wrote: Hi, I am trying to build a triclinic solvent box around two.pdb using the following commands editconf -bt triclinic -f two.pdb -o three.pdb -d 0.9 -box 20 10 10 genbox -cp three.pdb -cs spc216.gro -o four.pdb -p two.top However the generated pdb file four.pdb shows a cubic

[gmx-users] Solvent_box

Hi, I am trying to build a triclinic solvent box around two.pdb using the following commands editconf -bt triclinic -f two.pdb -o three.pdb -d 0.9 -box 20 10 10 genbox -cp three.pdb -cs spc216.gro -o four.pdb -p two.top However the generated pdb file four.pdb shows a cubic solvation box inst