[gmx-users] Free energy calculations (FEP) and soft core potential 1-1-48
Julian Zachmann
FrankJulian.Zachmann at uab.cat
Wed Jul 15 18:51:35 CEST 2015
It just crashes... Without any error message.
I am now re-running the simulations with fewer lambda points and for 5ns.
Let's see what comes up.
2015-07-15 18:12 GMT+02:00 Barnett, James W <jbarnet4 at tulane.edu>:
> Do you get any output with the crash? Or is it just a segmentation fault?
>
> --
> James “Wes” Barnett
> Ph.D. Candidate
> Chemical and Biomolecular Engineering
>
> Tulane University
> Boggs Center for Energy and Biotechnology, Room 341-B
> New Orleans, Louisiana 70118
> jbarnet4 at tulane.edu
> LinkedIn
>
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Julian
> Zachmann <FrankJulian.Zachmann at uab.cat>
> Sent: Wednesday, July 15, 2015 9:20 AM
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Free energy calculations (FEP) and soft core
> potential 1-1-48
>
> Dear Gromacs Users,
>
> I am running free energy calculations (FEP) to estimate relative binding
> affinities. So far, my results don't match the experimental results (not
> even close), so I must be doing something wrong.
>
> My protocol is the following:
>
> - Energy minimisation
> - Leap frog minimisation
> - 0.1ns NVT
> - 2ns Simulated Annealing up to 350K
> - 0.1ns NPT
> - 1ns MD production run
>
> During the whole equilibration time I am using umbrella pulling to maintain
> an interaction between one residue and the ligand (especially important
> during SA) but I remove it for MD because I am afraid it would influence my
> results (even though I don't know it for sure).
>
> The simulation time for 1ns is quite short of course but I have 'nstdhdl'
> put to 10 to get a lot of output.
>
> The other settings are pasted below. So far I was using 1-1-6 for the soft
> core potential but because the results were not good, I was thinking to try
> 1-1-48. However in this case the simulations always crash. Has anybody run
> successfully 1-1-48 soft core potentials in Gromacs and how did you chose
> your settings? Like me pasted below?
>
> Any other suggestions about what I am doing wrong?
> Could I maintain the pull distance constraint during the MD simulation?
>
> Best regards,
> Julian
>
> free_energy = yes
> init_lambda_state = $i
> ; 0 1 2 3 4 5 6
> 7 8 9 10 11 12 13 14 15 16 17
> 18 19 20 21 22 23 24 25 26 27 28
> 29 30 31 32 33 34 35 36 37 38
> 39 40 41 42 43 44 45 46 47 48 49
> 50 51 52 53 54 55 56 57 58 59 60
> 61 62 63 64 65 66 67 68 69 70
> 71 72 73 74 75 76 77 78 79 80 81
> 82 83 84 85 86 87 88 89 90 91 92
> 93 94 95 96 97 98 99
> fep_lambdas = 0.0000 0.0300 0.0600 0.0900 0.1200 0.1500 0.1800
> 0.2100 0.2400 0.2700 0.3000 0.3300 0.3600 0.3900 0.4200 0.4500 0.4800
> 0.5100 0.5400 0.5700 0.6000 0.6300 0.6600 0.6900 0.7200 0.7500 0.7800
> 0.8100 0.8400 0.8700 0.9000 0.9300 0.9600 1.0000 1.0000 1.0000 1.0000
> 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000
> 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000
> 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000
> 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000
> 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000
> 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000
> 1.0000 1.0000 1.0000
> vdw_lambdas = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
> 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
> 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
> 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0500 0.1000 0.1500
> 0.2000 0.2500 0.3000 0.3500 0.4000 0.4500 0.5000 0.5500 0.6000 0.6500
> 0.7000 0.7500 0.8000 0.8200 0.8500 0.8700 0.8800 0.8900 0.9000 0.9100
> 0.9200 0.9300 0.9350 0.9400 0.9450 0.9500 0.9530 0.9570 0.9600 0.9630
> 0.9670 0.9700 0.9730 0.9770 0.9800 0.9820 0.9840 0.9860 0.9880 0.9900
> 0.9910 0.9920 0.9930 0.9940 0.9950 0.9955 0.9960 0.9965 0.9970 0.9975
> 0.9980 0.9983 0.9987 0.9990 0.9992 0.9993 0.9994 0.9995 0.9996 0.9997
> 0.9998 0.9999 1.0000
> ; 1-1-6
> sc-coul = no
> sc-alpha = 0.5
> sc-power = 1
> sc-sigma = 0.3
> sc-r-power = 6
> ; 1-1-48
> ;sc-coul = no ;
> ;sc-alpha = 0.0025 ; either 0.5 (sc-r-power = 6) or
> 0.0025 (sc-r-power = 48)
> ;sc-power = 1 ; 1 or 2
> ;sc-sigma = 0.3 ; default 0.3
> ;sc-r-power = 48 ; possible 6, 48
> calc-lambda-neighbors = -1
> nstdhdl = 10
> dhdl-derivatives = yes
> separate-dhdl-file = yes
> --
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--
Julian Zachmann
Laboratori de Medicina Computacional
Unitat de Bioestadistica. Facultat de Medicina
Universitat Autonoma de Barcelona
08193 Bellaterra (Barcelona). Spain
Phone: (3493) 581 2797
Fax: (3493) 581 2344
E-mail: FrankJulian.Zachmann at uab.cat
http://lmc.uab.es
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