uhmm...is "rasmol" a program that do the analyses on data in the remote file "out.xyz" ?
If it is, "rasmol" is a local program on your machine ? If it is, then the only remote is the data file, right ?
if it is
then you have a couple of options:
1) transfer the data file "out.xyz" from remote machine to a local directory on your machine, using ftp or scp, smbclient, etc.
2) access the remote file on a networked folder using NFS or CIFS. This could impact on the network performance depending how the file is accessed by "rasmol" - Just one read on all file is fine; it won't hurt the network performance - otherwise, several small random access will.
You could provide more info for a more precise feedback.