[gmx-users] Re: gmx-users Digest, Vol 75, Issue 107

-- From: Sent: Tuesday, July 20, 2010 1:00 PM To: Subject: gmx-users Digest, Vol 75, Issue 107 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/

[gmx-users] Re: gmx-users Digest, Vol 75, Issue 107

-- From: Sent: Tuesday, July 20, 2010 1:00 PM To: Subject: gmx-users Digest, Vol 75, Issue 107 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/

[gmx-users] Ewald summation

hello gmx users I want to ask a couple of questions. 1) how gromacs calculates coulomb 14 interactions ; is it the same way as it calculates the other coulomb interactions; I want  Coulomb 1-4 to be calculated with eq 4.156 page 86 of manual v4.0 is it possible2) is the coulomb-SR part of the co

[gmx-users] Re: Energy miscalculation

hi gmx-users sorry for this pack of emails. the page has not a good format. you can find my text included to this email. thanks hi gmx-users In order to discover the miscalculation that gromacs computes in a system of 450 molecules in vacuum and after a gmx-user guidance i ran a simulation of o

[gmx-users] Re: Energy miscalculation

2) deleting the  [pairs] and all the lines below I)from md.log Step           Time         Lambda              0        0.0        0.0 Grid: 3 x 3 x 3 cellsLong Range LJ corr.: 3.8522e-03Long Range LJ corr.: Epot -0.00732091, Pres: -0.00379895, Vir: 0.00732091   Energies (kJ/mol)        

[gmx-users] Re: Energy miscalculation

3) deleting only the last line of the [pairs] I)from md.log Step           Time         Lambda              0        0.0        0.0 Grid: 3 x 3 x 3 cellsLong Range LJ corr.: 3.8522e-03Long Range LJ corr.: Epot -0.00732091, Pres: -0.00379895, Vir: 0.00732091   Energies (kJ/mol)          A

[gmx-users] Re: Energy miscalculation

1)leaving the top file as it is above I)from md.log Step           Time         Lambda              0        0.0        0.0 Grid: 3 x 3 x 3 cellsLong Range LJ corr.: 3.8522e-03Long Range LJ corr.: Epot -0.00732091, Pres: -0.00379895, Vir: 0.00732091   Energies (kJ/mol)          Angle Ryc

[gmx-users] Energy miscalculation

hi gmx-users In order to discover the miscalculation that gromacs computes in a system of 450 molecules in vacuum and after a gmx-user guidance i ran a simulation of one molecule in vacuum just to calculate by hand all the energies. the mdp file that i use is  ; VARIOUS PREPROCESSING OPTIONStitl

[gmx-users] Re: Energy miscalculation

3) deleting only the last line of the [pairs] I)from md.log Step           Time         Lambda              0        0.0        0.0 Grid: 3 x 3 x 3 cellsLong Range LJ corr.: 3.8522e-03Long Range LJ corr.: Epot -0.00732091, Pres: -0.00379895, Vir: 0.00732091   Energies (kJ/mol)        

Re: [gmx-users] Energy miscalculation

i did three simulations 1) leaving the top file as it is above2) deleting the  [pairs] and all the lines below3) deleting only the last line of the [pairs] the results with usage of the command gmxdump -s topol.tpr | lessfor step 0 are below 1)leaving the top file as it is above I)from md.log Ste

[gmx-users] Energy calculation

hi gmx-users In order to discover the miscalculation that gromacs computes in a system of 450 molecules in vacuum and after a gmx-user guidance i ran a simulation of one molecule in vacuum just to calculate by hand all the energies. the mdp file that i use is  ; VARIOUS PREPROCESSING OPTIONStitl

[gmx-users] Question about topologies

Hello [ atomtypes ];   type      mass    charge    ptype       c6            c12     CH3     15.035     0.000    A       9.0638e-3      2.5206e-5    CH2     14.027     0.000    A       5.8108e-3      2.2071e-5    CS2     14.027     0.000    A       5.8108e-3      2.2071e-5    OS      15.999     0

Re: [gmx-users] Positive Total energy

hi I did what you said to me but with a new system about 450 molecules in vacuum because i was given an equilibrated initial configuration. I also did a simulation with one molecule in vacuum just to compare. Simulation from 450 molecules with C12 = 3.325789e-7 Step Time L

[gmx-users] Positive Total energy

Hello  I have sent several emails and i am sorry. It is my last attempt to finish this simulation.The molecule i have is C-C-C-C-C-C-O-C-C-O-C-C-O-H or C10H1O3. (ciej molecule) I dont use gromacs librariesthe files i use are attached to the email in which i have descriped step by step the forcef

[gmx-users] Coulomb (SR) problem

hello again I had a problem with a sim of some molecules in vacuum and a gmx-user told me to do a simulation only in one molecule just to see what gromacs calculates and what does not. My problem concerned the sum of all energies in the system. After i did the sim with one molecule i found out

[gmx-users] extra non bonded interaction

hello I have a problem with C10O3H. The problem is that i use Trappe model and there you can add an extra repulsive interaction of molecule 10 (Oxygen) with molecule 14 (Hydrogen). The formula that TraPPE uses is 4E7/rij^12. with the transformation of 4E7in gromacs units (kJ*nm^12*mol-1) i tak