Hello gmx-users,
I am attempting to use g_analyze to find the error estimate on the average
volume of my system. Using an .xvg file with my volume data and the -ee flag I
receive the following message.
Found only 1 number on line, assuming no time is present.
Read 1 sets of 611700 points,
Justin A. Lemkul jalem...@vt.edu 3/18/2010 9:35 AM
Jacob Spooner wrote:
I am attempting a simulation of a drug molecule using the ffamber/gaff within
gromacs. When it comes to assigning charge groups the manual says that one
should group together nearby atoms and the groups should have
I am attempting a simulation of a drug molecule using the ffamber/gaff within
gromacs. When it comes to assigning charge groups the manual says that one
should group together nearby atoms and the groups should have a net integer
charge. Since AMBER charge parameters are obtained from QM
Hello,
I am planning to run some free energy of solvation calculations on a
drug/enzyme system. I want to start out with pen-G as my drug. I have found
that OPLS atoms 685-687 describe the beta-lactam portion of my drug, but I see
that they are left out of the gromacs ffopls**.itp/atp files.
Justin A. Lemkul jalem...@vt.edu 1/18/2010 3:23 PM
Jacob Spooner wrote:
Hello,
I am planning to run some free energy of solvation calculations on a
drug/enzyme system. I want to start out with pen-G as my drug. I have found
that OPLS atoms 685-687 describe the beta-lactam portion
van der Spoel sp...@xray.bmc.uu.se 5/19/2009 10:06 PM
Jacob Spooner wrote:
I am planning on using g_clustsize to do some condensation analysis. I
looked at g_cluster and see that it has a number of method options including
single linkage and jarvis patrick. Is it true that g_clustsize has
I am planning on using g_clustsize to do some condensation analysis. I looked
at g_cluster and see that it has a number of method options including single
linkage and jarvis patrick. Is it true that g_clustsize has only the single
linkage option? I took a look at the source code but this type
I am doing some simulations involving high pressure condensation of
hydrocarbons. I have read that Gromacs can be used for condensation analysis.
I have been looking at the g_cluster and g_clustsize commands, and I think that
they will be my tools. My main question is that if I am using
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