[gmx-users] principal component analysis

Dear all users I would like to calculate pc loadings for various integrated factors in the form of following sample table: Integrated Factors PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10 Total non polar surface area 0.60 -0.07 -0.76 -0.11 0.08 0.05 -0.16 0.08 -0.01 0.02 Native

Re: [gmx-users] principal component analysis

Hi Prathiba, I think you should have a look at the Functional Mode Analysis method from Bert de Groot's lab. Cheers, Tsjerk On Sat, Sep 28, 2013 at 8:13 AM, pratibha kapoor kapoorpratib...@gmail.comwrote: Dear all users I would like to calculate pc loadings for various integrated factors

[gmx-users] g_select problem

Hello: I am trying to analyze the water density along Z direction of my protein. Here is my g_select command: g_select_mpi -f ../md_pbc_center.xtc -s ../md.tpr -on density.ndx -sf select.dat and here is my select.dat: waterO = water and name OW and z30 and z70; close = water0 and within 0.4

Re: [gmx-users] g_select problem

Hi, I am not sure, but try resname SOL or something similar. Also, your first line has waterO and second line has water0. On Sat, Sep 28, 2013 at 1:00 PM, Albert mailmd2...@gmail.com wrote: Hello: I am trying to analyze the water density along Z direction of my protein. Here is my g_select

Re: [gmx-users] g_select problem

On 09/28/2013 09:42 AM, rajat desikan wrote: Hi, I am not sure, but try resname SOL or something similar. Also, your first line has waterO and second line has water0. Hi Rajat: thanks a lot for such kind and helpful comments. It works now. I run it by command: g_select_mpi -f

[gmx-users] Regarding atom numbering in .top and .gro files

Hi all, I want to put off constraint between some bonds in my system based on their atom numbers but the .gro file and .top file atom numbers do not match, because I used .pdb file to generate this .top file using pdb2gmx. (the top files contains the atom numbers based on this initial input .pdb

[gmx-users] OPLS/AA + TIP5P, anybody?

Dear Gigo: everything that I suggested was just ways that you might get a system without bad contacts to start your simulation with the proper (standard) tip5p model and oplsaa. I expected that combination to work together since they came out of the same lab, but looking at the initial tip5p

Re: [gmx-users] Regarding atom numbering in .top and .gro files

On 9/28/13 11:20 AM, bipin singh wrote: Hi all, I want to put off constraint between some bonds in my system based on their atom numbers but the .gro file and .top file atom numbers do not match, because I used .pdb file to generate this .top file using pdb2gmx. (the top files contains the

[gmx-users] Restarting simulation -s. files?

Hello gromacs users, I restarted my run due to power failure using mdrun -v -s .tpr -cpi .cpt, but the output files generating -s.gro , -s.tpr -s.xtc, how do I make it so it continues to update the original .xtc and .tpr files? Thanks, Xu Huang Research Assistant Chemical

Re: [gmx-users] Restarting simulation -s. files?

On 9/28/13 2:46 PM, Xu Dong Huang wrote: Hello gromacs users, I restarted my run due to power failure using mdrun -v -s .tpr -cpi .cpt, but the output files generating -s.gro , -s.tpr -s.xtc, how do I make it so it continues to update the original .xtc and .tpr files? If you're

Re: [gmx-users] Restarting simulation -s. files?

Justin, I see. Is there a way to *stitch* the two files together so I can continue onto a NPT run? On Sep 28, 2013, at 2:49 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/28/13 2:46 PM, Xu Dong Huang wrote: Hello gromacs users, I restarted my run due to power failure using mdrun -v -s

Re: [gmx-users] Restarting simulation -s. files?

On 9/28/13 2:52 PM, Xu Dong Huang wrote: Justin, I see. Is there a way to *stitch* the two files together so I can continue onto a NPT run? Appending is the default behavior of mdrun, if invoked properly and the files haven't been messed with. If not, trjcat appends trajectories and

Re: [gmx-users] Restarting simulation -s. files?

I see, Thank you for the information Justin. On Sep 28, 2013, at 2:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/28/13 2:52 PM, Xu Dong Huang wrote: Justin, I see. Is there a way to *stitch* the two files together so I can continue onto a NPT run? Appending is the default

Re: [gmx-users] OPLS/AA + TIP5P, anybody?

Dear Chris, I am really grateful for your help. This is what I did, with additional LJ terms on LP1 and LP2 of tip5p: - 5000 steps of steepest descent with positions restraints on protein and flexible water (flexibility like in tip4p), - 5000 steps of steep, no restraints, flexible water, -

[gmx-users] Adding hydrogen

Hi all users, Is it possible to add hydrogens to some of the selected atoms in the system using pdb2gmx? With best regards, Naser -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please

[gmx-users] OPLS/AA + TIP5P, anybody?

Dear Gigo: that's a good comprehensive testing and report. Please let us know what you find out from those authors. Their paper was short on methods (unless I missed it... I didn't check for any SI), so perhaps they did something non-standard and didn't report it. I think at this point it is a

[gmx-users] Deuterate organic solvent

I want to run a simulation of cyclohexane in deuterated chloroform. I was able to run a sim of cyclohexane in regular chloroform, but unable to find how to make a solvent deuterated. I know that pdb2gmx has a -heavyh and -deuterate option, would I do it this way? It isn't a protein and would