Re: [gmx-users] Generate many random configurations

I agree with you now. Thanks for your input. This was a very helpful conversation. I have decided to write my own program in Matlab. That being said, I assume there is a way to export files from Matlab to a .gro specific file format. Do you know if this is true or not? Thanks, Blake -- Vie

Re: [gmx-users] Generate many random configurations

You are right...it is physically unreasonable for the particles to occupy the same space. I will not be running any MD simulations with the configurations that I am generating. I will only use the configurations to determine the coordination number -- the goal is to emulate an ideal gas, but with

Re: [gmx-users] Generate many random configurations

I am generating x number of random configurations by iteratively calling the genbox command (implemented with a bash script), concatenating the results to obtain multiple random configurations, and calculating the g(r) over all configurations. So in a sense, I am calculating the g(r) over a trajec

Re: [gmx-users] Generate many random configurations

Thanks for your reply and helpful suggestions Justin. I have successfully implemented the concatenation command (after generating the desired number of configurations). There is another detail with which I am having trouble. So, I actually want to generate configurations in which it is possible

Re: [gmx-users] Generate many random configurations

I have figured out to accomplish what I want by writing a bash script. However, one thing I am still struggling with is determining how to concatenate the resulting configurations. There are two possible solutions: 1) concatenate multiple .gro files that have been generated at the end or 2) conca

[gmx-users] Generate many random configurations

As many of you probably know, genbox may be used to add additional solute molecules to a simulation box with a .gro output file containing the coordinates of initial and added solute atoms. Is it possible to do this many times (i.e. >1000) with a single output that contains the coordinates of all

Re: [gmx-users] order parameter

Is g_hydorder available only in certain versions of GROMACS? I am using version 4.5.3 and it says that g_hydorder is not found. Perhaps it is time to update. Blake -- View this message in context: http://gromacs.5086.x6.nabble.com/order-parameter-tp4455094p5014563.html Sent from the GROMACS Us

Re: [gmx-users] order parameter

I cannot locate the VMD script to calculate the tetrahedral order parameter. Does anyone know where I can find it? Alternatively, the manual states that g_order can compute this parameter, but it is not clear to me how to do so. It seems like this command is tailored for carbon tails. I would l

Re: [gmx-users] Carboxylate OPLS-AA parameters

Alternatively, I could use the parameters for a carboxylate head group, the neighboring CH2 group and then alcohol parameters for the rest of the CH2 groups and terminal CH3. This would probably make more sense. Does anyone else agree? -- View this message in context: http://gromacs.5086.x6.nab

Re: [gmx-users] Carboxylate OPLS-AA parameters

After looking at the parameters used for Asp and Glu, I have found that those are the ones I identified to use for my simulations of carboxylates. However, there is no terminal methyl group on Asp or Glu, like there is on a linear carboxylate. So, do you think it would be acceptable to use a term

Re: [gmx-users] Carboxylate OPLS-AA parameters

I understand now. Thank you very much for your help Justin. Blake -- View this message in context: http://gromacs.5086.x6.nabble.com/Carboxylate-OPLS-AA-parameters-tp5014043p5014058.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Plea

Re: [gmx-users] Carboxylate OPLS-AA parameters

I am now thoroughly confused. I have read papers that report the OPLS-AA sigma and epsilon values, as well as atom charges. The latter charges match those in the ffoplsaanb.itp file. I am not doing any fancy simulations and only want to compare basic information between simulations of butanoic a

Re: [gmx-users] Carboxylate OPLS-AA parameters

I obtained the charges from the oplsaanb.itp file in the gromacs/share/top directory. Do you know of a reference that provides the OPLS-AA parameters for Asp or Glu? -- View this message in context: http://gromacs.5086.x6.nabble.com/Carboxylate-OPLS-AA-parameters-tp5014043p5014052.html Sent from

Re: [gmx-users] Carboxylate OPLS-AA parameters

Thanks for that information. The problem I am encountering is that the sum of the charges of the carboxylate ion are not summing to -1. Below is a list of OPLS-AA parameters, including a description of the atom type and charge. Assume I am trying to make a topology file for butanoate. The numbe

[gmx-users] Carboxylate OPLS-AA parameters

Does anyone know of a paper that uses OPLS-AA parameters to simulate carboxylate ions in water? I am trying to determine the appropriate Lennard-Jones parameters (for the carboxylate ion) to use. Thanks, Blake Purdue University Department of Chemistry Ben-Amotz Research Lab -- View this messag

[gmx-users] Tables for user-defined potentials

What are the formatting requirements for tables to be used as user-defined potentials? I found the example tables, but cannot find the details in the manual. It would be useful to have the requirements so I can save the tables in the correct format when generated. Otherwise, does anyone have any

[gmx-users] grompp error - no molecules were defined in the system

When running grompp, I am receiving the error "No molecules were defined in the system." I have a relatively simple topology and .gro file. I cannot locate the source of the error. Does anyone have any suggestions? Here is an example of the .gro and .top file that I am using. Thanks. HSb