[gmx-users] Water removed from system and visualizing protein alone

Björn Sommer bjoern at CELLmicrocosmos.org
Fri Feb 5 11:26:12 CET 2016

On 5/02/2016 9:02 pm, gromacs.org_gmx-users-request at maillist.sys.kth.se 
> Hi,
> That works, but only if your full trajectory is small enough to fit in
> memory!
> Mark
> On Fri, 5 Feb 2016 09:05 Nikhil Maroli<scinikhil at gmail.com>  wrote:
>> >HI,
>> >simple way is to load the full trajectory and gro file then  change the
>> >water draw style and protein draw style,so that you can have a nice look
>> >on the structure,separately ..no need to remove anything from the .gro and
>> >tpr or xtc
>> >Regards
>> >Nikhil
>> >
>> >
Mark, yes, but you know that you can just skip every Xth frame in VMD by 
defining in the "Molecule File Browser" Frames -> Stride. Yes, it will 
not be so smooth anymore, but you can check at least if the trajectory 
meets your expectations. And as I said before, if your memory is very 
limited, please 1) load the PDB, then 2) select the molecules/atoms to 
be visualized in the "Representations" window, and then 3) load the 
trajectory (see my previous email for details). Especially in case you 
are not interested in the water, this may safe a lot of your precious 

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