-- Anirban Ghosh wrote: > Hi All, > I want to perform ED sampling along first principle > component in GROMACS. For that I am using the make_edi > command to generate the required .edi file to be > subsequently used in mdrun. But I cannot understand > the meaning of the algorithms -linfix, -linacc, > -radfix, -radacc and -radcon. What does fixed step > linear expansion and fixed step radius expansion > specify here?
as make_edi -h says: -linfix: perform fixed-step linear expansion along selected eigenvectors. -linacc: perform acceptance linear expansion along selected eigenvectors. (steps in the desired directions will be accepted, others will be rejected). -radfix: perform fixed-step radius expansion along selected eigenvectors. -radacc: perform acceptance radius expansion along selected eigenvectors. (steps in the desired direction will be accepted, others will be rejected). Note: by default the starting MD structure will be taken as origin of the first expansion cycle for radius expansion. If -ori is specified, you will be able to read in a structure file that defines an external origin. -radcon: perform acceptance radius contraction along selected eigenvectors towards a target structure specified with -tar.NOTE: each eigenvector can be selected only once. If you only want to constrain the position along the first eigenvector, linfix and linacc are probably the most meaningful options. With -linfix, you impose a predefined fixed stepsize per MD step (specified with -linstep). In that case, you could use something like: make_edi -f -s -n -linfix "1" -linstep "-0.0001" Using -linacc, you don't specify a fixed stepsize, but let the MD decide the stepsize. The only constraint that is applied in that case that (if you choose the forward direction as target) that backward steps are prohibited. In that case, use something like: make_edi -f -s -n -linfix "1" -accdir "1.0" (here the positive sign of the "accdir" argument specifies the direction). > How should I give the string options for > these algorithms see example above > and which one should I use? that we cannot answer for you. It all depends on the question you're trying to address with these simulations. Bert ______________________________________ Bert de Groot, PhD Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 37077 Goettingen, Germany tel: +49-551-2012308, fax: +49-551-2012302 http://www.mpibpc.mpg.de/groups/de_groot _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
