[gmx-users] free energy of complex system
Hi, I'm just trying to calculate free energy of a complex system using following method: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/03_workflow.html However, I'm facing some difficulties understanding how can I achieve the goal. The tutorial goes on with a single entity from lambda=0 to 1 with 0.05 spacing for data collection. Now, if I would like to calculate free energy of a complex (say, dimeric protein) then how am I supposed to design the lambda states ? I mean will it be like, one monomer will remain constant and the other monomer goes from lambda=0 to 1 state ? If that be the case then please suggest a way to customize the procedure. Please provide some suggestions. I'm really willing to apply this method in my scenario. Thank you. -- Abhisek Mondal *Senior Research Fellow* *Protein Crystallography Group* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA* -- 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] Values of coul_lambda for free energy calculation.
http://www.alchemistry.org/wiki/Constructing_a_Pathway_of_Intermediate_States#Avoid_turning_off_charges_and_Lennard-Jones_sites_at_the_same_time You don't disappear Lennard Jones interactions while charges are still there, charges are done first. 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 Wed, 29 Aug 2018 at 04:07, neelam wafa wrote: > > Hi gmx users, > I want to calculate free energy of binding for protein ligand complex. In > first step of free energy of solvation when i have to create lambda states > vwd_lambda changes from 0.00 and increases gradually to 1. Can the > coul_lambda be changed fradually after the vwd_lambda becomes 1. > > Kindly need your suggestions. > Regards > -- > 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.
Re: [gmx-users] Joining two simulation box into a big box
gmx editconf -translate Use that to shift each box to the correct coordinate space of the larger simulation box, by the appropriate axis dimension of each it is being stacked on. Join the gro files together using a text editor, removing header and footer for intermediate boxes, adjust atom count at top of gro file, adjust box dimensions appropriately at end of gro file. 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 Wed, 29 Aug 2018 at 02:42, Joydeep Munshi wrote: > > Hello, > > I am working with polymer-fullerene bulkheterojnction layers. Currently I > have a simulation box size of 20x20x17 nm with 3d PBC on. I have 25 of > these simulations with different velocity seeds. > > Now I want to join them together to make a 100x100x17 nm box and then > equillibrate the system accordingly. Following are a few questions: > > 1. How can I join them using gromacs commands and exisiting gro files?? > 2. Is this process physically/statistically reasonable ? and is it > satatistically same if I simulate the whole process starting with a > 100x100x17 nm box instead of joining them? > > Thank you and hope to get some answers. > > *Thanks and regards,* > *Joydeep Munshi,* > *Graduate Research Assistant,* > *Packard Lab 375,* > *Mechanical Engineering and Mechanics,* > *Lehigh University* > *Contact: (484)-821-6702* > -- > 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.
Re: [gmx-users] Values of coul_lambda for free energy calculation.
Sir Justin and sir Mark Please comment on my question. I ll be really thankful to you. On Tue, 28 Aug 2018, 11:07 pm neelam wafa, wrote: > Hi gmx users, > I want to calculate free energy of binding for protein ligand complex. In > first step of free energy of solvation when i have to create lambda states > vwd_lambda changes from 0.00 and increases gradually to 1. Can the > coul_lambda be changed fradually after the vwd_lambda becomes 1. > > Kindly need your suggestions. > Regards > -- 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] Values of coul_lambda for free energy calculation.
Hi gmx users, I want to calculate free energy of binding for protein ligand complex. In first step of free energy of solvation when i have to create lambda states vwd_lambda changes from 0.00 and increases gradually to 1. Can the coul_lambda be changed fradually after the vwd_lambda becomes 1. Kindly need your suggestions. Regards -- 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] Joining two simulation box into a big box
Hello, I am working with polymer-fullerene bulkheterojnction layers. Currently I have a simulation box size of 20x20x17 nm with 3d PBC on. I have 25 of these simulations with different velocity seeds. Now I want to join them together to make a 100x100x17 nm box and then equillibrate the system accordingly. Following are a few questions: 1. How can I join them using gromacs commands and exisiting gro files?? 2. Is this process physically/statistically reasonable ? and is it satatistically same if I simulate the whole process starting with a 100x100x17 nm box instead of joining them? Thank you and hope to get some answers. *Thanks and regards,* *Joydeep Munshi,* *Graduate Research Assistant,* *Packard Lab 375,* *Mechanical Engineering and Mechanics,* *Lehigh University* *Contact: (484)-821-6702* -- 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] Intramolecular interaction i don't know how to restraint by add intramol interaction to .top
I wonder how to find this intramol- interaction to add to .top i am calculate free energy for my protein ligand. And i stuck in step restraint. Help me Gửi từ điện thoại thông minh Samsung Galaxy của tôi. -- 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] Interaction energy with Reaction-field
Hello everyone,
this is my first time asking something in here, so I'm going to try to be as
clear as possible.
Im trying to calculate the electrostatic interaction energy of an ion with the
surrounding solvent (water) using a reaction-field scheme. Im interested to
know the interaction energy within R_c (cutoff) betweens these two groups, but
Im confused with the definitions when I run gmx energy. Which term should I be
looking for? RF-excl, Coul-SR:ION-SOL? both of them? What I bassically want to
know is the average value of equation 4.13 in the manual, for all pairs within
R_c, for these two groups
V_crf = f*q_i*q_j*[\frac{1}{r_ij} + k_rf*r^2_ij - c_rf]
I'm using a charged group scheme for this, and I have assigned the charged
group numbers explicitly in the topology.
Thank you for your time and help.
Best,
Javier.
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[gmx-users] Heterogeneous GPU cluster question?
Dear users (and developers), My sys. admin. is exploring purchasing some more GPU nodes for our cluster and was curious if we could get away with running GROMACS on a cluster that has two different types of GPUs, i.e. 70% of the nodes have 2 p100 gpus while 30% have volta (both have 2 gpu's per node).? I've been looking through the mailing list, but haven't bumped into this situation before. My inclination was to just purchase the "older" p100 since that is what all of the nodes are currently sporting, but thought I would ask to see if anyone has tried this kind of set-up before. Thanks, -Micholas === Micholas Dean Smith, PhD. MRSC Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: Tuesday, August 28, 2018 10:08 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] rerun doesn't calculate Coulomb & LJ interactions between groups On 8/28/18 10:04 AM, Irem Altan wrote: > Hi, > > I ran some umbrella sampling simulations on GPUs. I want to get the Coulomb > and LJ energy between certain groups (chain A - chain B, chain A - solvent, > etc.) , so I ran rerun: > gmx mdrun -rerun umbrella1.xtc -nb cpu -v -deffnm umbrella1 > However, when I run gmx energy on the output .edr file: > gmx energy -f umbrella1.edr -o umbrella1_ener.xvg > I only get 50 terms listed, as opposed to ~90 that contains things like > "LJ-SR:SOL-Chain_A". What am I missing? > The executable is created with the following command: > gmx grompp -f umbrella.mdp -c conf1.gro -p topol.top -n index.ndx -maxwarn 1 > -o umbrella1.tpr > where chain A, chain B, and SOL are defined in index.ndx. The contents of index.ndx are irrelevant unless you've actually specific which energygrps you want to define (in the .mdp file). Also, why are you using -maxwarn 1? This should almost never be done. -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. -- 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] rerun doesn't calculate Coulomb & LJ interactions between groups
On 8/28/18 10:04 AM, Irem Altan wrote: Hi, I ran some umbrella sampling simulations on GPUs. I want to get the Coulomb and LJ energy between certain groups (chain A - chain B, chain A - solvent, etc.) , so I ran rerun: gmx mdrun -rerun umbrella1.xtc -nb cpu -v -deffnm umbrella1 However, when I run gmx energy on the output .edr file: gmx energy -f umbrella1.edr -o umbrella1_ener.xvg I only get 50 terms listed, as opposed to ~90 that contains things like "LJ-SR:SOL-Chain_A". What am I missing? The executable is created with the following command: gmx grompp -f umbrella.mdp -c conf1.gro -p topol.top -n index.ndx -maxwarn 1 -o umbrella1.tpr where chain A, chain B, and SOL are defined in index.ndx. The contents of index.ndx are irrelevant unless you've actually specific which energygrps you want to define (in the .mdp file). Also, why are you using -maxwarn 1? This should almost never be done. -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.
[gmx-users] rerun doesn't calculate Coulomb & LJ interactions between groups
Hi, I ran some umbrella sampling simulations on GPUs. I want to get the Coulomb and LJ energy between certain groups (chain A - chain B, chain A - solvent, etc.) , so I ran rerun: gmx mdrun -rerun umbrella1.xtc -nb cpu -v -deffnm umbrella1 However, when I run gmx energy on the output .edr file: gmx energy -f umbrella1.edr -o umbrella1_ener.xvg I only get 50 terms listed, as opposed to ~90 that contains things like "LJ-SR:SOL-Chain_A". What am I missing? The executable is created with the following command: gmx grompp -f umbrella.mdp -c conf1.gro -p topol.top -n index.ndx -maxwarn 1 -o umbrella1.tpr where chain A, chain B, and SOL are defined in index.ndx. Best, Irem -- 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] rotation of atoms by more than 90 degrees & LINCS Warnings
Dear all, My system consists of 2 orthorhombic parallel graphene sheets in a big triclinic box filled with water. when i am trying to run equillibration then i am getting too many lincs warnings and simulation has been getting crashed everytime. i have put retraint on all atoms of graphene but still this problem is occuring again. My .mdp file looks like this title = OPLS Graphene IN WATER NVT equilibration define = -DPOSRES -DFLEXIBLE ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 50; 2 * 50 = 1000 ps dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 1.0 ps nstvout = 1000 ; save velocities every 1.0 ps nstenergy = 1000 ; save energies every 1.0 ps nstlog = 1000 ; update log file every 1.0 ps ; Bond parameters continuation= yes ; first dynamics run constraint_algorithm= lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy lincs-warnangle = 90 ; Neighborsearching vdw-modifier= Force-switch cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 10; 20 fs, largely irrelevant with Verlet rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 rlist = 1.2 ; short-range van der Waals cutoff (in nm) rvdw-switch = 1.0 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = nose-hoover ; nose-hoover thermostat tc-grps = GRA SOL ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC periodic-molecules = yes ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; number of steps for center of mass motion removal = comm-mode= Linear nstcomm = 1 comm-grps= GRA SOL ; Velocity generation gen_vel = no; assign velocities from Maxwell distribution gen_temp= 300 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed ;non equillibrium md freezegrps: GRA freezedim: Y Y Y i have tried various things but nothing is working. please help to solve this problem Regards Sagar Bathla -- 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.
