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From: | Jean-Noël Grad |
Subject: | Re: initial coordinates |
Date: | Thu, 02 Sep 2021 17:34:02 +0200 |
User-agent: | Roundcube Webmail/1.3.16 |
Dear Gulsah Gul,This can be achieved using the MDAnalysis python package. The user guide section "Reading various formats using MDAnalysis" shows how to populate an ESPResSo system with the C-alpha atoms of a protein from a PDB file:
https://espressomd.github.io/doc/io.html#reading-various-formats-using-mdanalysis Best, JN On 2021-09-02 05:54, Gulsah Gul wrote:
Hello all, I want to setup a system by introducing an initial coordinate file of molecules like .gro, .pdb etc. but I couldn't understand how to read it and how to assign it to the system.part.pos in python. Since there are several different bead types, also I couldn't get where should I define the bead types based on position id. Do you have any sample script or suggestion? Thank you Best
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