GROMACS version: 2020
GROMACS modification: No
Dear Esteemed Grommacs Users,
I am using grommacs suit to determine the electrostatic potential for the binary membrane lipid system (POPC:POPG) embedded with an antimicrobial peptide. My system is 50X50X100 Å in size with 26635 atoms and the peptide is 15 amino acids long. I am using the g_potential grommacs analysis tool that doubly integrates poisson’s equation by splitting my simulation box along the z-axis (100 Å) into slices and thereby calculating the charge density in each slice.
Problem:
Applying the gmx_potential analysis on my trajectory using the command provided below, I get an output with the first column representing the Z-axis (10 nm) and the second column represents the electrostatic potential profile of my system. However, from the results obtained 1nm is represented by 5 points and these differ by 0.19 nm and that is 1.90 Å.
What can be done to reduce the 5 points in 1 nm so that each 1 nm is represented by only one point .
The command Used is as shown below:
gmx potential -f F13_10_popc_popg.gro -n index.ndx -s F13_10_popc_popg.tpr -o f13_potential.xvg -sl 50
0 -0
0.1911076009273529 -0.003975429859264937
0.3822152018547058 -0.008806811165285639
0.5733228027820587 -0.005261333334216065
0.7644304037094116 0.0005557325938832618
0.9555380046367645 -0.000527984628960897
1.146645605564117 -0.00956722287286349
1.33775320649147 -0.0243821745696698
1.528860807418823 -0.03441102929013167
1.719968408346176 -0.02506378005169613
1.911076009273529 0.0160069652490727
2.102183610200882 0.104203195757509
2.293291211128235 0.2244917122160982
2.484398812055588 0.3176864293699357
2.675506412982941 0.3503485162825999
2.866614013910294 0.3434129238068704
3.057721614837646 0.3373145156195056
3.248829215764999 0.3589220894433759
3.439936816692352 0.4084268581773411
3.631044417619705 0.4671289766923796
3.822152018547058 0.5030787203295112
4.013259619474411 0.4913009200248702
4.204367220401764 0.4430527129153139
4.395474821329117 0.3912022693404811
4.58658242225647 0.3570248841474277
4.777690023183823 0.3491498426487559
4.968797624111176 0.3592679092354664
5.159905225038528 0.3500601732521442
5.351012825965881 0.285350442835314
5.542120426893234 0.1681440814206822
5.733228027820587 0.04688834489589302
5.92433562874794 -0.03619070797569603
6.115443229675293 -0.08507792228567089
6.306550830602646 -0.1092615281630147
6.497658431529999 -0.1210999305128742
6.688766032457352 -0.137329104763267
6.879873633384705 -0.1536491912378248
7.070981234312057 -0.1613190526681917
7.26208883523941 -0.1617707172929246
7.453196436166763 -0.1598253275123188
7.644304037094116 -0.1593940203606093
7.835411638021469 -0.1620131776488123
8.026519238948822 -0.1656907420703806
8.217626839876175 -0.1736938843010221
8.408734440803528 -0.1845650593255952
8.599842041730881 -0.1878936995832629
8.790949642658234 -0.1831415497384798
8.982057243585587 -0.1806174785144635
9.173164844512939 -0.1883331518341926
9.364272445440292 -0.1977842502805291
Thank you very much for your kind assistance.