[gmx-users] problem when install gromacs on a node of cluster

Hey all, I wanted to install gromacs on one node of a cluster. Firstly I downloaded all needed packages to /home/william/software, then unpack all of them under this folder. Then, I followed the " Quick and Dirty Installation" instruction using following commands: export SOFT=$HOME

[gmx-users] insert silicon atoms into ice structure

Dear GMXusers, I wanna insert several silicon atoms into an ice crystal. I use genbox with a Silicon.pdb, but there's no any silicon atom in the out file. Do I miss anything? Anyone has some comments? Thanks a lot. Best, william Here's output log: r...@xwei:~/Desktop/gromacs/ice

[gmx-users] Re: insert silicon atoms into ice structure

Thanks for reply. I intended to add these silicon atoms into ice structure, the Santan William wrote: > Dear GMXusers, > I wanna insert several silicon atoms into an ice crystal. I use > genbox with a Silicon.pdb, but there's no any silicon atom in the out > file. D

[gmx-users] Re: insert silicon atoms into ice structure (Justin A. Lemkul)

any other way to insert silicon atoms into a solid ice structure? Thanks a lot. Best, william Santan William wrote: > Dear GMXusers, > I wanna insert several silicon atoms into an ice crystal. I use > genbox with a Silicon.pdb, but there's no any silicon atom in the out &g

[gmx-users] protein crystallization

Hello, users. Can Gromacs do protein crystallization simulations? I tried looking for some information about it on mailings but failed. Would anyone give me some advice how to do it? Thanks. Best, william ___ gmx-users mailing listgmx-users@gromacs.o

[gmx-users] can gmx be used to simulation NaCl

hi gmx users, Can Gromacs be used to simulate NaCl crystallization and melting? If it could, where can I find pdb/top/itp etc. input files? Thanks in advance. Best regards, William ___ gmx-users mailing listgmx-users@gromacs.org http://www.g

[gmx-users] how to fix molecules and give different temperature

Dear users, I want to do a simulation as below configuration: BOX1BOX2BOX3 3 boxes are contacting with their neighbors in x direction. BOX1 and BOX2 are ice crystal, BOX3 is water. I want to fix molecules in BOX1 and BOX3, so they will not move during simulation. And BOX1

[gmx-users] how to fix molecules and give different temperature

Dear users, I want to do a simulation as below configuration: BOX1BOX2BOX3 3 boxes are contacting with their neighbors in x direction. BOX1 and BOX2 are ice crystal, BOX3 is water. I want to fix molecules in BOX1 and BOX3, so they will not move during simulation. And BOX1

RE: [gmx-users] RE: how to fix molecules and give different temperature

Hi Vitaly, Thanks for your reply. Do fixed molecules have a temperature? What temperature is in fact? Yeah, I want to give all fixed molecules a temperature. The temperature in left box is 253K, in right box is 283K. So there is 30K gradient between these two boxes. The

RE:[gmx-users] RE: how to fix molecules and give different temperature

Hi Vitaly, Thanks for your reply. Do fixed molecules have a temperature? What temperature is in fact? Yeah, I want to give all fixed molecules a temperature. The temperature in left box is 253K, in right box is 283K. So there is 30K gradient between these two boxes. The

[gmx-users] can GMX be used to simulate metal or alloy melting and solidification

Hi users, I checked the mailing list and website, and didn't find any information about metal or alloy MD simulation by Gromacs. Can GMX be used to simulate metal or alloy melting and solidification? Best regards, William ___ gmx-users mailing

[gmx-users] how to make ice crystal by TIP4P, TIP5P water model

Hi gmx users, Online available ice.pdb has following contents. I think it is made for SPC water model. How can I make ice structure for TIP4P, TIP5P water model? Thanks, HEADERA beautiful Ice Ih crystal REMARKGenerated by mkice with the following options: REMARKnx = 5, ny