Re: [gmx-users] Ryckaert-Bellemans type dihedral

Suman Chakrabarty wrote: Hi, I need to write my own topology file for a system using Ryckaert-Bellemans type dihedral potential. Since I should remove the 1-4 non-bonded interaction in this case, I wanted to know whether it is enough not to keep any [ pairs ] entry in the topology file (manual p

[gmx-users] reg MOPAC/gromacs installations

Dear sir/Madam   thanks in Advance                        i Did dos2unixconversions. as u saiid . but still i get error when i run the same output configure in command prompt of Redhat linux5 as followschecking for a BSD-compatible install... /usr/bin/install -c checking whether build environmen

Re: [gmx-users] how to use atom2cg.awk

Dear sir : how to motify the $5 in details? Thank you! --- 09年5月8日，周五, Justin A. Lemkul 写道： 发件人: Justin A. Lemkul 主题: Re: [gmx-users] how to use atom2cg.awk 收件人: "Discussion list for GROMACS users" 日期: 2009年5月8日,周五,下午6:46 xi zhao wrote: > > > Dear Sirs: >   I wang to know simulate

Re: [gmx-users] how to use atom2cg.awk

xi zhao wrote: Dear sir : how to motify the $5 in details? Thank you! Use a text editor (vi, emacs, gedit, etc), like you would to create any script. -Justin 4 --

Re: [gmx-users] reg MOPAC/gromacs installations

vidhya sankar wrote: Dear sir/Madam * thanks in Advance* i Did dos2unixconversions. as u saiid . but still i get error when i run the same output configure in command prompt of Redhat linux5 as follows checking for a BSD-compatible install... /usr/bin/install -c chec

[gmx-users] Are Gromos 45a3 and GROMOS 53a6 compatible?

Hi GROMOS 45a3 force field GROMOS 53a6 force field Are they compatible? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before

Re: [gmx-users] Are Gromos 45a3 and GROMOS 53a6 compatible?

Chih-Ying Lin wrote: Hi GROMOS 45a3 force field GROMOS 53a6 force field Are they compatible? Try reading the papers that describe them. See GROMACS manual for references. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.

[gmx-users] introducing constrain

Dear sir, I want to put a constrain into my system. I am simulating lipid bilayer membrane by GROMACS. I want to put a virtual wall at the z-axis in my system so that no lipid can move through the virtual wall. In a code language, it is just this : for lipid :if z < 60

[gmx-users] Warning: Pressure scaling more than 1%.

Dear all, when I run position-restrained simulation (total 15000steps). when it reached 740 steps Step 741 Warning: Pressure scaling more than 1%. Step 742 Warning: Pressure scaling more than 1%. Step 743 Warning: Pressure scaling more than 1%. Step 744 Warning: Pressure scaling more than

Re: [gmx-users] Warning: Pressure scaling more than 1%.

Zhanglin Ni wrote: Dear all, when I run position-restrained simulation (total 15000steps). when it reached 740 steps Step 741 Warning: Pressure scaling more than 1%. Step 742 Warning: Pressure scaling more than 1%. Step 743 Warning: Pressure scaling more than 1%. Step 744 Warning: Pressu