Mark,<br><br><div class="gmail_quote"><div> </div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div bgcolor="#FFFFFF" text="#000000">If you make your layer boundaries perpendicular to
some axis then you can use position restraints on water oxygens that
have non-zero force constants only with respect to that axis. Then
relax the water position restraints before any others.<div class="im"><br></div></div></blockquote><div><br>Yes, I've thought about this to apply posres onto selected coordinates to allow waters move only laterally relavitely protein-membrane-like system. But this prevent to move water into the receptor interious as well so it's not very good aproach. <br>
<br>Also I've thought about vary of the ref_t oprions wich I've defined separatelly for protein_membrane layer and for water_ions. As I've told I want to increase confoprmation sampling of my protein by means of gradually temperature increasing. Could I rise only ref_t for the protein_ccl4 layer with the apllied posres on the protetn (backbone atoms) and ccl4 ( C atoms) during nvt equilibration while not changing ref_t for water and ions ? Will my system be some unphysicall in that case ? Or as the alternative way could I decrease ref_t for the water_ions layer in the end of nvt equilibration to allow water to move out from the Ccl4 layer?<br>
<br><br><br>James<br></div></div>