Re: [gmx-users] Arginine_Hydrochloride topology

shahid nayeem wrote: Dear All I am trying to find the topology and parameterof free Arginine Hydrchloride molecule in gromacs force-field format. Developing it in Pro-Drg will not serve as I will need some other parametrization tool to check it charges. If someone can help, I will be

[gmx-users] re-equilbrating membrane protein system after g_membed and ligand addition

I was looking at the g_membed paper recently, and noticed the authors only spent 10ns to re-equilibrate the membedded-system after g_membeding. This they also did after bumping the temperature from 300 to 323K to prevent ordering of the bilayer even though the typical simulation temperatures of

Re: [gmx-users] re-equilbrating membrane protein system after g_membed and ligand addition

Peter C. Lai wrote: I was looking at the g_membed paper recently, and noticed the authors only spent 10ns to re-equilibrate the membedded-system after g_membeding. This they also did after bumping the temperature from 300 to 323K to prevent ordering of the bilayer even though the typical

Re: [gmx-users] re-equilbrating membrane protein system after g_membed and ligand addition

On 2011-07-29 07:25:08AM -0500, Justin A. Lemkul wrote: Peter C. Lai wrote: I was looking at the g_membed paper recently, and noticed the authors only spent 10ns to re-equilibrate the membedded-system after g_membeding. This they also did after bumping the temperature from 300 to 323K

Re: [gmx-users] trjconv problem for two groups

Liu Shiyong wrote: Dear all, I tried to output protein-ligand complex from trr file . Could I select both Group 2 and Group 12 at the same time ? Or I have to run this command for every group , respectively? Use make_ndx to merge the groups and pass the index file to trjconv. -Justin

[gmx-users] Dimensionless units question

Hi all, I'm trying to calculate the force on one particle and the total electrostatic energy of my system, which consists of a lattice of 25 evenly spaced charges in the xy plane and a single charge in the center above to preserve charge neutrality. The reference values I have been given are in

[gmx-users] PRODRG tools

Dear all, Is there any other free tool like PRODRG ? PRODRG server couldn't read PDB file from user any more. It 's not easy to get a free version asap. Best Shiyong -- Shiyong Liu -- Biomolecular Physics and Modeling

Re: [gmx-users] PRODRG tools

Liu Shiyong wrote: Dear all, Is there any other free tool like PRODRG ? PRODRG server couldn't read PDB file from user any more. It 's not easy to get a free version asap. You can contact the maintainers for a standalone version of PRODRG. Then you can run it whenever you want.

Re: [gmx-users] Dimensionless units question

Hi, reduced units works for LJ particles only. I am not sure if it works when you include electrostatics. When you set charge = 1 it is 1electronic charge. I would suggest not to use the reduced units for LJ in this scenario. Amit On Fri, Jul 29, 2011 at 8:05 AM, Alex Marshall amars...@uwo.ca

Re: [gmx-users] Dimensionless units question

Hi Amit, So if I understand you correctly, any LJ interaction I impose on these particles will be quite arbitrary because I'm only concerned with electrostatics, right? How then might I go about comparing the dimensionless reference values given with the values I calculated? I don't think I can

Re: [gmx-users] Dimensionless units question

I am not sure what you want to measure. You mentioned that force and energy I calculate are still quite far from the reference values, now are you only looking at electrostatic contributions to these or the total contributions? If its total contribution then LJ parameters should also be correct

Re: [gmx-users] Dimensionless units question

I'm trying to calculate the total electrostatic energy of the system, and the force in the Z direction on the particle placed above the lattice. It's a purely electrostatic problem, ideally LJ shouldn't come into it at all, but I don't know how else to convert the resulting energy and force to

Re: [gmx-users] Dimensionless units question

On Fri, Jul 29, 2011 at 12:14 PM, Alex Marshall amars...@uwo.ca wrote: I'm trying to calculate the total electrostatic energy of the system, and the force in the Z direction on the particle placed above the lattice. It's a purely electrostatic problem, ideally LJ shouldn't come into it at all,

Re: [gmx-users] PRODRG tools

Actually, you can use other parametrization tools like antechamber (for amber) or cgenff (for charmm). Liu Shiyong wrote: Dear all, Is there any other free tool like PRODRG ? PRODRG server couldn't read PDB file from user any more. It 's not easy to get a free version asap. You can

[gmx-users] cannot open file

Hi gromacs users,   I'm running a simulation but I keep getting the following errors. rogram mdrun_mpi, VERSION 4.5.1 Source code file: gmxfio.c, line: 537 Can not open file: taExcited.tpr For more information and tips for troubleshooting, please check the GROMACS website at

[gmx-users] umbrella sampling

Hi, I used umbrella sampling method to restrain the distance of two molecules at several distances. Then I can use g_wham to get the free energy as a function of the distance. Is there any way that I can get the free energy as a function of another parameter? Thanks a lot. Sincerely, Qian

Re: [gmx-users] umbrella sampling

Dear Email Sender, Thank you very much for contacting me! Unfortunately, I am not available in the office at the moment and cannot respond to your email. I will be able to handle your request starting again Thursday, August 4, 2011. For all questions about CloudBroker and the CloudBroker

Re: [gmx-users] umbrella sampling

Qian Wang wrote: Hi, I used umbrella sampling method to restrain the distance of two molecules at several distances. Then I can use g_wham to get the free energy as a function of the distance. Is there any way that I can get the free energy as a function of another parameter? Thanks a

Re: [gmx-users] cannot open file

Taylor Kaplan wrote: Hi gromacs users, I'm running a simulation but I keep getting the following errors. rogram mdrun_mpi, VERSION 4.5.1 Source code file: gmxfio.c, line: 537 Can not open file: taExcited.tpr For more information and tips for troubleshooting, please check the GROMACS

[gmx-users] citation

Hello all, Can anyone tell me how gromacs may be cited besides Principal Papers 1. Berendsen, et al. (1995) *Comp. Phys. Comm.* *91: *43-56. (DOIhttp://dx.doi.org/doi:10.1016/0010-4655%2895%2900042-E_, Citations of this paperhttp://scholar.google.com/scholar?cites=6703762643559347673hl=en

Re: [gmx-users] citation

Elisabeth wrote: Hello all, Can anyone tell me how gromacs may be cited besides Principal Papers 1. Berendsen, et al. (1995) /Comp. Phys. Comm./ *91: *43-56. (DOI http://dx.doi.org/doi:10.1016/0010-4655%2895%2900042-E_, Citations of this paper

[gmx-users] umbrella sampling

format your data for 2D-WHAM with 1D being the distance and the 2nd-D being your other coordinate of interest. Specify a value of zero for the force constants for your 2nd-D. Run 2D-WHAM. Boltzmann project the 2D PMF onto your 2nd-D. I think you can also do essentially the same thing by

[gmx-users] OPLSAA parameters

Hello to all, I am looking for bonded and nonbonded parameters for C H atoms in saturated hydrocarbons. atom types are: Carbon atoms opls_135 opls_136 H opls_140 opls_135 12.01100 ; alkane CH3 opls_136 12.01100 ; alkane CH2 opls_1401.00800 ; alkane H. Please help me out