Re: [gmx-users] The energy minimization....

Hi, Mark:I have done the energy minimization and simulation of ATP in vacuum individual ( Maybe you have suggested me to do this yesterday, but actually I did not understand it, and just do this in solution).There are following problems:1. in the energy minimization, the potential energy is

Re: [gmx-users] GAP parameter

Dear Mark, Thank you and sorry. From parameters of oplsaa and quantum calculations, I have been building all force field parameters for GAP. Cheers On Fri, 17 Aug 2007, Mark Abraham wrote: Osmair Vital de Oliveira wrote: Dear Mark, Thank you for the helpful!!. For instance, I have

[gmx-users] how to get CVS version gmx?

Dear gmx users developers, Would you please let me know how to get the gmx CVS version? I registered in gmx website, however, everytime I try to view the link *instructions on how to access our CVS repository*http://www.gromacs.org/index.php?option=com_contenttask=viewid=80Itemid=99, it

Re: [gmx-users] The energy minimization....

Hi you need to explain in detail what steps you are doing before the minimisation and also what parameters you are using in your .mdp file because i have just run a minimisation of ATP (in water) to test the topology in the GROMOS96 ff and it works fine for me, so there must be a problem in

Re: [gmx-users] how to get CVS version gmx?

Hi Linda, you can use these commands to download from CVS: cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs login Then hit RETURN on password prompt cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs co gmx Carsten Zhaoyang Fu wrote: Dear gmx users developers, Would you

Re: [gmx-users] The energy minimization....

The end structure is the same as the start because gromacs cannot find a lower energy structure than the initial one. This indicates something severely wrong, either with the topology or starting structure. You could get a better idea of what's going on by telling gromacs to output structures

[gmx-users] Generalized order parameter S2

Hello gmx-users, I have a query regarding the generalized order paprameter S2.I have performed a 50ns simulation of a protein in solution.I now want to calculate the order parameter S2 of the protein from the trajectory.I looked through the mailing list to get an idea on how to go

[gmx-users] Re : long-term drift and crash

The same bugs occurs during the NPT equilibration stage that I did after the energy minimization (with l-bgfs, till convergence), the average pressure being now -0.5 bar (over the 200 ps the simulation ran before it crashed). Still the same things : everything I plot with g_energy is normal, the

[gmx-users] Step size too small

Dear gmx-users, I have 2 molecules in a box, as usual pdb2gmx saw them as one. i edited the .top file to remove the bonds created between the two molecules, I also added a distance restraint btw the molecules. (The 2 structures have been separately minimized). However, I get the ff message

Re: [gmx-users] Step size too small

Hello! Check out http://wiki.gromacs.org/index.php/Errors#Stepsize_too_small. 2C_or_no_change_in_energy._Converged_to_machine_precision. 2C_but_not_to_the_requested_precision Cheers /Per 17 aug 2007 kl. 18.28 skrev Sheyore Omovie: Dear gmx-users, I have 2 molecules in a box, as usual

Re: [gmx-users] Pull code methods?

Hi Maik, Thank you for the answer. I still have some questions. I still didn't get the umberalla sampling method. It seems to me AFM and umberalla are the same except that in umberalla we dont define a Pull rate. Looking at the literature, people have been using umberalla method with discrete

Re: [gmx-users] Step size too small

Hi, I do not think that what Per suggests is the problem, if you look at the potential energy after the minimisation this value is huge (and the other two values are inf!). The problem is most likely with your topology. As you say the two molecules have been successfully minimised on their

[gmx-users] Pressure coupling and tau_p values

Hello, I am simulating a lipid bilayer system under a shear stress, in which I am interested in looking at the surface tension. I have done a number of simulations in an NPT ensemble using semiisotropic Berendsen pressure coupling. For a system such as this, I am wondering what would be an

[gmx-users] job magic number in MXMPI_MAGIC

Thanks Tom, I have tried that in the past though, and I still get Epot values of nan. It seems the only other option I have is to place the molecules in separate boxes, set disre=simple, and use the -multi option during the mdrun. The -multi option only works with the parallel installation.

[gmx-users] Re: \[gmx\-users\] The energy minimization\.\.\.\. (fwd)

Hi Also please keep emails on the list, it helps everyone (you getting more people's opinion than just mine, and people who may have a similar problem in the future) Tom Forwarded Message Date: 18 August 2007 02:29 +0100 From: TJ Piggot [EMAIL PROTECTED] To: [EMAIL

Re: [gmx-users] job magic number in MXMPI_MAGIC

Sheyore Omovie wrote: Thanks Tom, I have tried that in the past though, and I still get Epot values of nan. One solution is to take your (successful) individual .top files and edit them in line with the example in chapter 5 to create .itp files for your two molecules. Then include them both

Re: [gmx-users] Re : long-term drift and crash

BON Michael wrote: The same bugs occurs during the NPT equilibration stage that I did after the energy minimization (with l-bgfs, till convergence), the average pressure being now -0.5 bar (over the 200 ps the simulation ran before it crashed). Still the same things : everything I plot with

[gmx-users] Pressure coupling and tau_p values

For example, a 3ns simulation using a tau_p of 0.5 I get a surface tension of 30 dynes/cm and using a tau_p of 5.0 I get a surface tension of 25 dynes/cm. First thing that comes to mind is that your area per lipid is not at equilibrium. Assuming that your bilayer normal lies in the Z