[gmx-users] gromacs.org_gmx-users Digest, Vol 152, Issue 61

Michael K. Gilson mgilson at ucsd.edu
Sun Dec 18 21:34:39 CET 2016


Hi Mark,

Is the lowest drift in Figure 3.5, ~1e-6 kj/mol/atom/ps, as good as it 
gets?

If the drift can be further reduced, how would one do this?

Thanks,
Mike

On 12/17/2016 11:29 PM, 
gromacs.org_gmx-users-request at maillist.sys.kth.se wrote:
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> Today's Topics:
>
>     1. Re: Energy conservation in NVE (Mark Abraham)
>     2. Re: Energy conservation in NVE (Mark Abraham)
>     3. Re: Problem in running energy minimization in Gromacs 5.1.2
>        version (#SUKRITI GUPTA#)
>     4. Re: Problem in running energy minimization in Gromacs 5.1.2
>        version (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 18 Dec 2016 05:04:57 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Energy conservation in NVE
> Message-ID:
> 	<CAMNuMASa6nqyDPp+9dL2LpWb4DoK_DLmteFv07__Coof+Tw9HA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> It's unclear from your description. See eg fig 3.5 from the reference
> manual. Be sure you have not ignored grompp warnings.
>
> Mark
>
> On Sun, 18 Dec 2016 14:28 Michael Gilson <mgilson at ucsd.edu> wrote:
>
>> For NVE simulations of a protein-ligand system in water, with
>> lincs-iter=4 and lincs-iter=5, we see ongoing, linear energy drift with
>> slopes of about -0.02 kJ/mol/ps and 0.01 kJ/mol/ps, respectively. Is
>> this about what you'd expect, or can we aim for better?
>>
>> Thanks,
>> Mike Gilson
>>
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
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>> send a mail to gmx-users-request at gromacs.org.
>>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 18 Dec 2016 05:04:57 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Energy conservation in NVE
> Message-ID:
> 	<CAMNuMASa6nqyDPp+9dL2LpWb4DoK_DLmteFv07__Coof+Tw9HA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> It's unclear from your description. See eg fig 3.5 from the reference
> manual. Be sure you have not ignored grompp warnings.
>
> Mark
>
> On Sun, 18 Dec 2016 14:28 Michael Gilson <mgilson at ucsd.edu> wrote:
>
>> For NVE simulations of a protein-ligand system in water, with
>> lincs-iter=4 and lincs-iter=5, we see ongoing, linear energy drift with
>> slopes of about -0.02 kJ/mol/ps and 0.01 kJ/mol/ps, respectively. Is
>> this about what you'd expect, or can we aim for better?
>>
>> Thanks,
>> Mike Gilson
>>
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 18 Dec 2016 06:25:33 +0000
> From: #SUKRITI GUPTA# <SUKRITI002 at e.ntu.edu.sg>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Problem in running energy minimization in
> 	Gromacs 5.1.2	version
> Message-ID:
> 	<KL1PR01MB10931466984C1D9D805A5EEAE79E0 at KL1PR01MB1093.apcprd01.prod.exchangelabs.com>
> 	
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
>
> Can anyone please help.
>
>
> Regards
>
> Sukriti
>
> [https://sixprd0111.outlook.com/owa/service.svc/s/GetFileAttachment?id=AAMkADNjYmY4NDc0LTVjMzUtNDNmOC1hYzdkLTU5NTZhODkwYjVhNwBGAAAAAACBUPJnHBz9Qb1jEGoiHu01BwCW%2B40K8EMKR52f2bViS6X0AAAANaBFAAC1PvQTaUN0S5CzEDGS8lwUAAIr8o3VAAABEgAQAIhFug57qj9Lg6WQKih11Lg%3D&X-OWA-CANARY=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.&retryCount=3]
>
> Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI at N) | Nanyang Technological University
> N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
> Tel: (65) 81164191 GMT+8h | Email:sukriti002 at e.ntu.edu.sg | Web:erian.ntu.edu.sg<http://www.ntu.edu.sg/home/xuzc/People.html>
>
>
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of #SUKRITI GUPTA# <SUKRITI002 at e.ntu.edu.sg>
> Sent: Friday, December 16, 2016 4:27:41 PM
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Problem in running energy minimization in Gromacs 5.1.2 version
>
> This sender failed our fraud detection checks and may not be who they appear to be. Learn about spoofing at http://aka.ms/LearnAboutSpoofing
>
> Dear all,
>
>
> I was running my gromacs simulations on Gromacs 4.5.5 version but my system got updated and it changed to Gromacs 5.1.2. No when I run the same energy minimization file as earlier but just adding cutoff-scheme = Verlet, my energy minimization is not running. Following is the message I get from Gromacs:
>
>
> Low-Memory BFGS Minimizer:
>     Tolerance (Fmax)   =  1.00000e+01
>     Number of steps    =         5000
> Using 10 BFGS correction steps.
>
>     F-max             =  2.21705e+05 on atom 295
>     F-Norm            =  1.25724e+04
>
> Step 0, Epot=1.569290e+03, Fnorm=8.461e+03, Fmax=1.134e+05 (atom 295)
>
> Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 10 (which may not be possible for your system). It
> stopped because the algorithm tried to make a new step whose size was too
> small, or there was no change in the energy since last step. Either way, we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.
>
> Double precision normally gives you higher accuracy, but this is often not
> needed for preparing to run molecular dynamics.
>
> writing lowest energy coordinates.
>
> Back Off! I just backed up v_b4pr.gro to ./#v_b4pr.gro.3#
>
> Low-Memory BFGS Minimizer converged to machine precision in 0 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  =  1.5692902e+03
> Maximum force     =  1.1339475e+05 on atom 295
> Norm of force     =  8.4610078e+03
>
> NOTE: 18 % of the run time was spent in pair search,
>        you might want to increase nstlist (this has no effect on accuracy)
>
> However, if I run energy minimization of the same file in version 4.5.5, energy minimization takes place and I do not encounter any error. Can anyone please help me with this? My energy minimization mdp file is as follows:
>
> ; VARIOUS PREPROCESSING OPTIONS
> title                    =
> cpp                      = /lib/cpp
> include                  =
> define                   = -DFLEXIBLE
>
> ; RUN CONTROL PARAMETERS
> integrator               = l_bfgs
> ; Start time and timestep in ps
> tinit                    = 0
> dt                       = 0.001
> nsteps                   = 5000
> ; For exact run continuation or redoing part of a run
> init_step                = 0
> ; mode for center of mass motion removal
> comm-mode                = Linear
> ; number of steps for center of mass motion removal
> nstcomm                  = 1
>
> ; ENERGY MINIMIZATION OPTIONS
> ; Force tolerance and initial step-size
> emtol                    = 10
> emstep                   = 0.01
> ; Max number of iterations in relax_shells
> niter                    = 20
> ; Step size (1/ps^2) for minimization of flexible constraints
> fcstep                   = 0
> ; Frequency of steepest descents steps when doing CG
> nstcgsteep               = 1000
> nbfgscorr                = 10
>
> ; OUTPUT CONTROL OPTIONS
> ; Output frequency for coords (x), velocities (v) and forces (f)
> nstxout                  = 100
> nstvout                  = 100
> nstfout                  = 100
> ; Checkpointing helps you continue after crashes
> nstcheckpoint            = 1000
> ; Output frequency for energies to log file and energy file
> nstlog                   = 100
> nstenergy                = 100
> ; Output frequency and precision for xtc file
> nstxtcout                = 0
> xtc-precision            = 1000
> ; This selects the subset of atoms for the xtc file. You can
>
> ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
> cutoff-scheme = Verlet
> nstlist                  = 10
> ; ns algorithm (simple or grid)
> ns-type                  = Grid
> ; Periodic boundary conditions: xyz (default), no (vacuum)
> ; or full (infinite systems only)
> pbc                      = xyz
> ; nblist cut-off
> rlist                    = 1.1
> domain-decomposition     = no
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
>
> coulombtype              = PME
> rcoulomb                 = 1.1
> ; Method for doing Van der Waals
> vdw-type                 = Switch
> ; cut-off lengths
> rvdw-switch              = 0.8
> rvdw                     = 1.1
> ; Apply long range dispersi0n corrections for Energy and Pressure
> DispCorr                 = No
> ; Extension of the potential lookup tables beyond the cut-off
> table-extension          = 2
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing           = 0.12
> ; FFT grid size, when a value is 0 fourierspacing will be used
> fourier_nx               = 0
> fourier_ny               = 0
> fourier_nz               = 0
> ; EWALD/PME/PPPM parameters
> pme_order                = 4
> ewald_rtol               = 4e-05
> ewald_geometry           = 3d
>
> epsilon_surface          = 0
> optimize_fft             = no
>
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen-vel                  = no
> gen-temp                 = 300
> gen-seed                 = 173529
>
> freezegrps = V
> freezedim = Y Y Y
>
>
>
> Thanks and Regards
>
>
> Sukriti
>
> [https://sixprd0111.outlook.com/owa/service.svc/s/GetFileAttachment?id=AAMkADNjYmY4NDc0LTVjMzUtNDNmOC1hYzdkLTU5NTZhODkwYjVhNwBGAAAAAACBUPJnHBz9Qb1jEGoiHu01BwCW%2B40K8EMKR52f2bViS6X0AAAANaBFAAC1PvQTaUN0S5CzEDGS8lwUAAIr8o3VAAABEgAQAIhFug57qj9Lg6WQKih11Lg%3D&X-OWA-CANARY=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.&retryCount=3]
>
> Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI at N) | Nanyang Technological University
> N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
> Tel: (65) 81164191 GMT+8h | Email:sukriti002 at e.ntu.edu.sg | Web:erian.ntu.edu.sg<http://www.ntu.edu.sg/home/xuzc/People.html>
>
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>
>
> ------------------------------
>
> Message: 4
> Date: Sun, 18 Dec 2016 07:29:31 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Problem in running energy minimization in
> 	Gromacs 5.1.2 version
> Message-ID:
> 	<CAMNuMAReM7OzCeta+WW8F3ii3ut+gh4PEH=aSk7h6Nf8eOgAGA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> You have a minimized structure (somehow). What happens when you use it as
> the starting point in the newer version?
>
> Mark
>
> On Sun, 18 Dec 2016 17:26 #SUKRITI GUPTA# <SUKRITI002 at e.ntu.edu.sg> wrote:
>
>> Hi,
>>
>>
>> Can anyone please help.
>>
>>
>> Regards
>>
>> Sukriti
>>
>> [
>> https://sixprd0111.outlook.com/owa/service.svc/s/GetFileAttachment?id=AAMkADNjYmY4NDc0LTVjMzUtNDNmOC1hYzdkLTU5NTZhODkwYjVhNwBGAAAAAACBUPJnHBz9Qb1jEGoiHu01BwCW%2B40K8EMKR52f2bViS6X0AAAANaBFAAC1PvQTaUN0S5CzEDGS8lwUAAIr8o3VAAABEgAQAIhFug57qj9Lg6WQKih11Lg%3D&X-OWA-CANARY=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.&retryCount=3
>> ]
>>
>> Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI at N)
>> | Nanyang Technological University
>> N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
>> Tel: (65) 81164191 GMT+8h | Email:sukriti002 at e.ntu.edu.sg | Web:
>> erian.ntu.edu.sg<http://www.ntu.edu.sg/home/xuzc/People.html>
>>
>>
>>
>> ________________________________
>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of #SUKRITI
>> GUPTA# <SUKRITI002 at e.ntu.edu.sg>
>> Sent: Friday, December 16, 2016 4:27:41 PM
>> To: gromacs.org_gmx-users at maillist.sys.kth.se
>> Subject: [gmx-users] Problem in running energy minimization in Gromacs
>> 5.1.2 version
>>
>> This sender failed our fraud detection checks and may not be who they
>> appear to be. Learn about spoofing at http://aka.ms/LearnAboutSpoofing
>>
>> Dear all,
>>
>>
>> I was running my gromacs simulations on Gromacs 4.5.5 version but my
>> system got updated and it changed to Gromacs 5.1.2. No when I run the same
>> energy minimization file as earlier but just adding cutoff-scheme = Verlet,
>> my energy minimization is not running. Following is the message I get from
>> Gromacs:
>>
>>
>> Low-Memory BFGS Minimizer:
>>     Tolerance (Fmax)   =  1.00000e+01
>>     Number of steps    =         5000
>> Using 10 BFGS correction steps.
>>
>>     F-max             =  2.21705e+05 on atom 295
>>     F-Norm            =  1.25724e+04
>>
>> Step 0, Epot=1.569290e+03, Fnorm=8.461e+03, Fmax=1.134e+05 (atom 295)
>>
>> Energy minimization has stopped, but the forces have not converged to the
>> requested precision Fmax < 10 (which may not be possible for your system).
>> It
>> stopped because the algorithm tried to make a new step whose size was too
>> small, or there was no change in the energy since last step. Either way, we
>> regard the minimization as converged to within the available machine
>> precision, given your starting configuration and EM parameters.
>>
>> Double precision normally gives you higher accuracy, but this is often not
>> needed for preparing to run molecular dynamics.
>>
>> writing lowest energy coordinates.
>>
>> Back Off! I just backed up v_b4pr.gro to ./#v_b4pr.gro.3#
>>
>> Low-Memory BFGS Minimizer converged to machine precision in 0 steps,
>> but did not reach the requested Fmax < 10.
>> Potential Energy  =  1.5692902e+03
>> Maximum force     =  1.1339475e+05 on atom 295
>> Norm of force     =  8.4610078e+03
>>
>> NOTE: 18 % of the run time was spent in pair search,
>>        you might want to increase nstlist (this has no effect on accuracy)
>>
>> However, if I run energy minimization of the same file in version 4.5.5,
>> energy minimization takes place and I do not encounter any error. Can
>> anyone please help me with this? My energy minimization mdp file is as
>> follows:
>>
>> ; VARIOUS PREPROCESSING OPTIONS
>> title                    =
>> cpp                      = /lib/cpp
>> include                  =
>> define                   = -DFLEXIBLE
>>
>> ; RUN CONTROL PARAMETERS
>> integrator               = l_bfgs
>> ; Start time and timestep in ps
>> tinit                    = 0
>> dt                       = 0.001
>> nsteps                   = 5000
>> ; For exact run continuation or redoing part of a run
>> init_step                = 0
>> ; mode for center of mass motion removal
>> comm-mode                = Linear
>> ; number of steps for center of mass motion removal
>> nstcomm                  = 1
>>
>> ; ENERGY MINIMIZATION OPTIONS
>> ; Force tolerance and initial step-size
>> emtol                    = 10
>> emstep                   = 0.01
>> ; Max number of iterations in relax_shells
>> niter                    = 20
>> ; Step size (1/ps^2) for minimization of flexible constraints
>> fcstep                   = 0
>> ; Frequency of steepest descents steps when doing CG
>> nstcgsteep               = 1000
>> nbfgscorr                = 10
>>
>> ; OUTPUT CONTROL OPTIONS
>> ; Output frequency for coords (x), velocities (v) and forces (f)
>> nstxout                  = 100
>> nstvout                  = 100
>> nstfout                  = 100
>> ; Checkpointing helps you continue after crashes
>> nstcheckpoint            = 1000
>> ; Output frequency for energies to log file and energy file
>> nstlog                   = 100
>> nstenergy                = 100
>> ; Output frequency and precision for xtc file
>> nstxtcout                = 0
>> xtc-precision            = 1000
>> ; This selects the subset of atoms for the xtc file. You can
>>
>> ; NEIGHBORSEARCHING PARAMETERS
>> ; nblist update frequency
>> cutoff-scheme = Verlet
>> nstlist                  = 10
>> ; ns algorithm (simple or grid)
>> ns-type                  = Grid
>> ; Periodic boundary conditions: xyz (default), no (vacuum)
>> ; or full (infinite systems only)
>> pbc                      = xyz
>> ; nblist cut-off
>> rlist                    = 1.1
>> domain-decomposition     = no
>>
>> ; OPTIONS FOR ELECTROSTATICS AND VDW
>> ; Method for doing electrostatics
>>
>> coulombtype              = PME
>> rcoulomb                 = 1.1
>> ; Method for doing Van der Waals
>> vdw-type                 = Switch
>> ; cut-off lengths
>> rvdw-switch              = 0.8
>> rvdw                     = 1.1
>> ; Apply long range dispersi0n corrections for Energy and Pressure
>> DispCorr                 = No
>> ; Extension of the potential lookup tables beyond the cut-off
>> table-extension          = 2
>> ; Spacing for the PME/PPPM FFT grid
>> fourierspacing           = 0.12
>> ; FFT grid size, when a value is 0 fourierspacing will be used
>> fourier_nx               = 0
>> fourier_ny               = 0
>> fourier_nz               = 0
>> ; EWALD/PME/PPPM parameters
>> pme_order                = 4
>> ewald_rtol               = 4e-05
>> ewald_geometry           = 3d
>>
>> epsilon_surface          = 0
>> optimize_fft             = no
>>
>> ; GENERATE VELOCITIES FOR STARTUP RUN
>> gen-vel                  = no
>> gen-temp                 = 300
>> gen-seed                 = 173529
>>
>> freezegrps = V
>> freezedim = Y Y Y
>>
>>
>>
>> Thanks and Regards
>>
>>
>> Sukriti
>>
>> [
>> https://sixprd0111.outlook.com/owa/service.svc/s/GetFileAttachment?id=AAMkADNjYmY4NDc0LTVjMzUtNDNmOC1hYzdkLTU5NTZhODkwYjVhNwBGAAAAAACBUPJnHBz9Qb1jEGoiHu01BwCW%2B40K8EMKR52f2bViS6X0AAAANaBFAAC1PvQTaUN0S5CzEDGS8lwUAAIr8o3VAAABEgAQAIhFug57qj9Lg6WQKih11Lg%3D&X-OWA-CANARY=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.&retryCount=3
>> ]
>>
>> Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI at N)
>> | Nanyang Technological University
>> N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
>> Tel: (65) 81164191 GMT+8h | Email:sukriti002 at e.ntu.edu.sg | Web:
>> erian.ntu.edu.sg<http://www.ntu.edu.sg/home/xuzc/People.html>
>>
>>
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
> ------------------------------
>

-- 
Michael K. Gilson, M.D., Ph.D.
Professor, Skaggs School of Pharmacy and Pharmaceutical Sciences
UC San Diego
9500 Gilman Drive
La Jolla, CA 92093-0736
voice: 858-822-0622
http://gilson.ucsd.edu
http://bindingdb.org
http://drugdiscovery.ucsd.edu
http://drugdesigndata.org



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