[gmx-users] g_analyze negative

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, dt

Re: [gmx-users] charge group assignment with AMBER parameters

>>> "Justin A. Lemkul" 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 nearb

[gmx-users] charge group assignment with AMBER parameters

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 calcu

Re: [gmx-users] OPLS AA simulation of beta-lactam system

>>> "Justin A. Lemkul" 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

[gmx-users] OPLS AA simulation of beta-lactam system

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.

Re: [gmx-users] g_clustsize method

>>> David van der Spoel 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 th

[gmx-users] g_clustsize method

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

[gmx-users] Condensation analysis

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 g_clu