Re: [gmx-users] Rupture force definition
Thanks Justin, I want to see the change statistically by using same parameter (velocity and same spring constant) Hence, I think it will be better to pull the same system by choosing its different conformation. Eg. I had taken the the last conformation of production md ( 50 ns) for pulling. Then in order to see the differences we can take conformation at 40th ns and apply the pull with same parameter (Same velocity and same spring constant ). On Mon, May 20, 2019 at 6:07 PM Justin Lemkul wrote: > > > On 5/17/19 6:15 AM, Rakesh Mishra wrote: > > Dear Justin > > > > After long time again I want to ask one question. > > If suppose I want to repeat the same production > > simulation ( final md simulation) for different seeds, > > then how to do. Because as from the knowledge of > > gromacs there is no manual way to put different seeds > > in the .mdp files. > > gen-seed gives you different starting velocities. If you want to perform > independent simulations they need to either start from (1) different > velocities, (2) different conformations, or (3) different pull vectors. > > -Justin > > > > > On Mon, Jun 25, 2018 at 7:27 PM Justin Lemkul wrote: > > > >> > >> On 6/25/18 8:48 AM, Rakesh Mishra wrote: > >>> Dear Justin. > >>> > >>> I have observed one thing that during pulling (Constant velocity > pulling > >> ) > >>> of dsDNA/dsRNA ( globally say Nucleic acid ) along helical direction, > we > >>> observe that in the force/time .xvg file, some time force value is +ve > >> and > >>> some time force value is -ve. So why it happens. In my thinking it > should > >>> always be +ve. > >> Free energy surfaces are rugged. Some intermediate conformations may > >> result in local free energy wells. > >> > >> -Justin > >> > >>> On Mon, Jun 11, 2018 at 5:37 PM, Justin Lemkul > wrote: > >>> > On 6/8/18 2:52 AM, Rakesh Mishra wrote: > > > Dear Justin . > > I have two query > > > > 1-What can be the optimized value of rate can be taken > > for pulling of dsDNA/dsRNA using gromacs format where solvent is > >> aqua. > >From your umbrella sampling manual, rate is very high like (0.01 > >> nm/ps), > > which is equal to 0.0001Angstrom/fs. > > > You'll note in the SI we tested lower values and achieved the same > outcome, so you need to test a few to be sure that whatever pull rate > >> you > impose does not introduce artifacts. There is no way, a priori, to > know > what an "optimized" rate would be. That term also has multiple > interpretations. > > 2- In pulling mdp file no random seed is discussed. But if we want to > > obtain 2 or 3 different trajectory during > > pulling ( of the same system ) for different seed, then how > to > >> give > > different seed in pulling mdp file. > > > > Note - In my thinking in gromacs, gen_seed = -1 is default value. > >> And > > it > > comes , when NVT is applied ( where > > velocity generation is allowed, to achieve required > > temperature through maxwell distribution ). But in case of pulling, > >> where > > no velocity > > generation is allowed . Then how to calculate > different > > pulling simulation of the same system for different seeds. > > > One does not supply a new random seed when doing a continuation of a > >> run. > If you want to start new simulations in each window or in multiple > replicates of a run, then use "gen_seed = -1" to get a completely > random > seed based on the process ID. > > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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-requ...@gromacs.org. > > >>> > >> -- > >> == > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Virginia Tech Department of Biochemistry > >> > >> 303 Engel Hall > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalem...@vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> == > >> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mail
Re: [gmx-users] FW: Free energy of solvation using the Bar method
Hi Shekhovtsov, Thank you very much. Kind regards, Riccardo -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Artem Shekhovtsov Sent: Monday, June 3, 2019 4:39 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] FW: Free energy of solvation using the Bar method Hello, Try to swap vdw_lambdas and coul_lambdas in *.mdp file like this: coul_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 vdw_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 Possible explanation: http://www.alchemistry.org/wiki/Constructing_a_Pathway_of_Intermediate_States#Avoid_turning_off_charges_and_Lennard-Jones_sites_at_the_same_time Best regards, Shekhovtsov Artem On Mon, Jun 3, 2019 at 5:23 PM Innocenti Malini, Riccardo < riccardo.innocentimal...@empa.ch> wrote: > > Dear all, > > I am currently trying to calculate the free energy of solvation for a > small hydrophobic molecule in water using the OPLSaa force field, > however for vdw lambda values above 0.2 my system continuously explodes. > > Before starting the free energy calculations I equilibrated the system > (100 ps in NVT and 4 ns in NPT ensemble). Then before starting the > free energy calculations before each lambda point I minimized the > energy using first the steepest descent method and then L-BFGS. The > system is then simulated in the NVT ensemble where it tends to blows > when the vdw for Lambda = 0.3. Below this value the system works fine > in simulations of up to 8 ns and the system appears to be equilibrated. > > I am not sure why this is happening. Would anybody have any advice? > Here is the free energy section of the mdp file: > > free_energy = yes > couple-moltype = Other > couple-lambda0 = vdw-q > couple-lambda1 = none > couple-intramol = no > init-lambda = -1 > init_lambda_state= 3 > delta_lambda = 0 > nstdhdl = 10 > fep-lambdas = > mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 > 0.00 0.00 > coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.05 0.10 > 0.15 > 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 > 0.90 > 0.95 1.00 > vdw_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 > 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 1.00 1.00 > 1.00 > 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 > 1.00 > 1.00 1.00 > bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 > 0.00 0.00 > restraint_lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 > 0.00 0.00 > temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 > 0.00 0.00 > calc_lambda_neighbors= 1 > init-lambda-weights = > dhdl-print-energy= no > sc-alpha = 0.5 > sc-power = 1 > sc-r-power = 6 > sc-sigma = 0.3 > sc-coul = no > separate-dhdl-file = yes > dhdl-derivatives = yes > dh_hist_size = 0 > dh_hist_spacing = 0.1 > > Thank you in advance for your help. > > Kind regards, > Riccardo > > -- > 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-requ...@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-requ...
Re: [gmx-users] oplsaa tooology for urea
If you are in the directory: …./share/gromacs/top And type: grep -iRL "URE" ./ You will get a list of all the files that contain "ure". With my installation of 2019.2 there are two files within oplsaa.ff "ffbonded.itp" and "atomtypes.atp" from which you use to easily build a urea.itp. You can alos use the urea.itp as a template from one of the other forcefields if you haven't built one from scratch before. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Tue, 4 Jun 2019 at 08:28, Alex wrote: > > Hi all, > > I do have a topology for urea from TPP, but, to use the terminology > frequently used here, "i have a DOUBT." ;) > Before I have gone into the full literature scouring mode, my DOUBT brought > me to this: > https://www.researchgate.net/post/Please_provide_me_ureagro_and_ureaitp_files_for_MDS > For the life of me, I can't find any rtp entries related to urea in > oplsaa.ff, which is my FF of choice. > > Justin, any thoughts? > > Thanks, > > Alex > -- > 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-requ...@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-requ...@gromacs.org.
[gmx-users] oplsaa tooology for urea
Hi all, I do have a topology for urea from TPP, but, to use the terminology frequently used here, "i have a DOUBT." ;) Before I have gone into the full literature scouring mode, my DOUBT brought me to this: https://www.researchgate.net/post/Please_provide_me_ureagro_and_ureaitp_files_for_MDS For the life of me, I can't find any rtp entries related to urea in oplsaa.ff, which is my FF of choice. Justin, any thoughts? Thanks, Alex -- 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-requ...@gromacs.org.
Re: [gmx-users] FW: Free energy of solvation using the Bar method
Hello, Try to swap vdw_lambdas and coul_lambdas in *.mdp file like this: coul_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 vdw_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 Possible explanation: http://www.alchemistry.org/wiki/Constructing_a_Pathway_of_Intermediate_States#Avoid_turning_off_charges_and_Lennard-Jones_sites_at_the_same_time Best regards, Shekhovtsov Artem On Mon, Jun 3, 2019 at 5:23 PM Innocenti Malini, Riccardo < riccardo.innocentimal...@empa.ch> wrote: > > Dear all, > > I am currently trying to calculate the free energy of solvation for a > small hydrophobic molecule in water using the OPLSaa force field, however > for vdw lambda values above 0.2 my system continuously explodes. > > Before starting the free energy calculations I equilibrated the system > (100 ps in NVT and 4 ns in NPT ensemble). Then before starting the free > energy calculations before each lambda point I minimized the energy using > first the steepest descent method and then L-BFGS. The system is then > simulated in the NVT ensemble where it tends to blows when the vdw for > Lambda = 0.3. Below this value the system works fine in simulations of up > to 8 ns and the system appears to be equilibrated. > > I am not sure why this is happening. Would anybody have any advice? Here > is the free energy section of the mdp file: > > free_energy = yes > couple-moltype = Other > couple-lambda0 = vdw-q > couple-lambda1 = none > couple-intramol = no > init-lambda = -1 > init_lambda_state= 3 > delta_lambda = 0 > nstdhdl = 10 > fep-lambdas = > mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 > coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.05 0.10 0.15 > 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 > 0.95 1.00 > vdw_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 > 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 1.00 1.00 1.00 > 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 > 1.00 1.00 > bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 > restraint_lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 > temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 > calc_lambda_neighbors= 1 > init-lambda-weights = > dhdl-print-energy= no > sc-alpha = 0.5 > sc-power = 1 > sc-r-power = 6 > sc-sigma = 0.3 > sc-coul = no > separate-dhdl-file = yes > dhdl-derivatives = yes > dh_hist_size = 0 > dh_hist_spacing = 0.1 > > Thank you in advance for your help. > > Kind regards, > Riccardo > > -- > 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-requ...@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-requ...@gromacs.org.
[gmx-users] FW: Free energy of solvation using the Bar method
Dear all, I am currently trying to calculate the free energy of solvation for a small hydrophobic molecule in water using the OPLSaa force field, however for vdw lambda values above 0.2 my system continuously explodes. Before starting the free energy calculations I equilibrated the system (100 ps in NVT and 4 ns in NPT ensemble). Then before starting the free energy calculations before each lambda point I minimized the energy using first the steepest descent method and then L-BFGS. The system is then simulated in the NVT ensemble where it tends to blows when the vdw for Lambda = 0.3. Below this value the system works fine in simulations of up to 8 ns and the system appears to be equilibrated. I am not sure why this is happening. Would anybody have any advice? Here is the free energy section of the mdp file: free_energy = yes couple-moltype = Other couple-lambda0 = vdw-q couple-lambda1 = none couple-intramol = no init-lambda = -1 init_lambda_state= 3 delta_lambda = 0 nstdhdl = 10 fep-lambdas = mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 vdw_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 restraint_lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 calc_lambda_neighbors= 1 init-lambda-weights = dhdl-print-energy= no sc-alpha = 0.5 sc-power = 1 sc-r-power = 6 sc-sigma = 0.3 sc-coul = no separate-dhdl-file = yes dhdl-derivatives = yes dh_hist_size = 0 dh_hist_spacing = 0.1 Thank you in advance for your help. Kind regards, Riccardo -- 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-requ...@gromacs.org.
