[gmx-users] Problem with restart simulation
Dear groamcs users I want to restart my MD simualtion. I have used this command: mdrun -s myname.trp -cpi myname.cpi -append but I know that are generated new file like: md.log state.cpt traj.trr ecc.. There is a keyword that rewrites the files, without that new files are generated? or Can I merge the files (example: myname.edr ener.edr or myname.trr traj.trr) once the simulation is over? Best regards D.V. -- 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] Problem with Umbrella Sampling simulation
of simulation. Best regards, D.V. 2016-07-22 14:23 GMT+02:00 Justin Lemkul <jalem...@vt.edu>: > > > On 7/22/16 8:19 AM, Daniele Veclani wrote: > >> Dear Gromacs Users >> >> I'm trying to calculate the potential mean force between two molecules (A >> and B). >> >> I created the various configurations through the pull simulation. To do >> this I kept fixes the position of the molecule A (position restraint) >> >> I have extracted the coordinates and sampled the various configurations. >> >> Now I have to use these configurations as input for umbrella sampling >> simulation. >> >> I have a couple of questions: >> >> - Do I have to maintain a position restraint on A molecule? >> >> > No. > > - Do I have to enter the position restraint even for molecule B? (Otherwise >> during the dynamic simulation I a change of the distance between molecule >> A >> and B) >> >> > No. The distance between A and B is all that matters and it is restrained > using the harmonic potential applied by the pull code. It will vary over > time but should on average, in each window, be equal to the restraint > reference distance specified in the .mdp file. > > -Justin > > - Can I get a clear explanation about this last step of the job? >> >> Best regards, >> D.V. >> >> > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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] How to fix molecules in gromacs?
Dear Justin Thanks for the answer. You can also give me an advice on this problem: I did as you told me. I used POSRES_0PCZ in .top file and -DPOSRES_0PCZ in .mdp file. But I find this error (grompp): "Atom index (1457) in position_restraints out of bounds (1456)" This is probably due to the fact that my posre.itp file is: ; position restraints for 0PCZ of cnt-cipro [ position_restraints ] ; i funct fcxfcyfcz 431 1000 1000 1000 441 1000 1000 1000 . . 14571 1000 1000 1000 14581 1000 1000 1000 14591 1000 1000 1000 14601 1000 1000 1000 . . 14961 1000 1000 1000 14971 1000 1000 1000 14981 1000 1000 1000 This file was built with genrestr. how can I solve this problem? Best regards, D.V. 2016-07-17 15:21 GMT+02:00 Justin Lemkul <jalem...@vt.edu>: > > > On 7/16/16 8:35 AM, Daniele Veclani wrote: > >> Dear gromacs users. >> >> I'm trying to fix a molecule inside the box. I want to use this molecule >> as >> an immobile reference in the pulling simulations. >> >> I can i do this? I have to use the position restraint or freezing Group? >> >> I tried to use position restraint, but, by analyzing the trajectories, >> I see that >> the molecule out of the box. >> >> This is my .top file: >> --- >> ; Topology of CNT and CFX >> ;--- >> #include "gromos54a7_atb.ff/forcefield.itp" >> >> ;--- >> ; Uncomment the line with needed topology below >> ;--- >> ; #include "zw" >> >> #include "cipro.itp" >> >> ; #include cnt >> >> #include "nano.itp" >> #ifdef DPOSRES_0PCZ >> #include "cnt-posre.itp" >> #endif >> >> #include "gromos54a7_atb.ff/spce.itp" >> >> [ system ] >> cnt-cipro >> [ molecules ] >> ; Compoundnmols >> AUT8 1 >> 0PCZ 1 >> SOL 39030 >> >> This is may .mdp file: >> >> ;preprocessing >> define = -DPOSRES_0PCZ >> > > Your syntax is wrong. The "-D" prefix needs to be added to whatever the > #ifdef keyword is. So for your topology to work, you need "define = > -DDPOSRES_0PCZ" > > Or, you can use -DPOSRES_0PCZ with #ifdef POSRES_0PCZ. > > You can check that no restraints are functioning by looking in the .log > file, as you will find no "Position Rest." energy term. If the restraints > are active, the associated energy is written. > > -Justin > > > ; Run control >> integrator = sd ; Langevin dynamics >> dt = 0.002 >> nsteps = 30; 0.6 ns >> nstcomm = 10 >> ; Output control >> nstxout = 5000 >> nstvout = 5000 >> nstfout = 5000 >> nstlog = 5000 >> nstenergy= 5000 >> nstxout-compressed = 5000 >> ; Neighborsearching and short-range nonbonded interactions >> cutoff-scheme= verlet >> nstlist = 10 >> ns_type = grid >> pbc = xyz >> rlist= 0.8 >> ; Electrostatics >> coulombtype = PME >> rcoulomb = 1.2 >> ; van der Waals >> vdwtype = cutoff >> rvdw = 1.2 >> ; Apply long range dispersion corrections for Energy and Pressure >> DispCorr = EnerPres >> ; Spacing for the PME/PPPM FFT grid >> fourierspacing = 0.12 >> ; EWALD/PME/PPPM parameters >> pme_order= 6 >> ewald_rtol = 1e-06 >> epsilon_surface = 0 >> ; Temperature coupling >> ; tcoupl is implicitly handled by the sd integrator >> tcoupl = Nose-Hoover >> tc_grps = system >> tau_t= 1.0 >> ref_t= 298.15 >> ; Pressure coupling is on for pull >> Pcoupl = Parrinello-Rahman >> tau_p= 0.5 >> compressibility = 4.5e-05 >> ref_p= 1.0 >> ; Free energy control stuff >> ; Generate velocities to start >> gen_vel
[gmx-users] Pulling: Fix the position of a molecule
Dear Gromacs Users I'm simulating a system of two molecule (A,B unbound). Right now, I am trying to generate the configurations and then make Umbrella Sampling Simulations. I have this problem: While I generate the configurations I observed that the molecule A comes out of the box and makes the calculation fail. I've used the position restraint generating posre.itp file for molecule A, but analyzing the trajectories I see that the molecule A moves and comes out of the box. How can I fix the problem? I attached my files for the topology, and poste.itp .mdp I use Gromacs 5.0.4. Best regards. D.V. -- 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] Domain Decomposition does not support simple neighbor searching.
Dear Gromacs Users I'm trying to do a simulation in a NVE ensemble in vaccum. But I but I find this error: "Domain Decomposition does not support simple neighbor searching, use grid searching or run with one MPI rank" If I use ns_type=grid I can generate the .tpr file, But when I run mdrun I find: "NOTE: This file uses the deprecated 'group' cutoff scheme. This will be removed in a future release when 'verlet' supports all interaction forms. and mdrun program crashes. How can I do energy minimization and simulation in NVE ensemble in vaccum with GROMACS 5.0.4? This is my .mdp file for energy minimization: ; Run control integrator = steep nsteps = 50 ; EM criteria and other stuff emtol= 10 emstep = 0.001 niter= 20 nbfgscorr= 10 ; Output control nstlog = 1 nstenergy= 1 ; Neighborsearching PARAMETERS cutoff-scheme= group vdw-type = Cut-off nstlist = 1; 10 fs ns_type = grid ; search neighboring grid cells pbc = No rlist= 0.0 ; short-range neighborlist cutoff (in nm) rlistlong= 0.0 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = cut-off ; Particle Mesh Ewald for long-range electrostatics rcoulomb-switch = 0 rcoulomb = 0.0; short-range electrostatic cutoff (in nm) rvdw = 0.0; short-range van der Waals cutoff (in nm) rvdw-switch = 0.0 epsilon_r= 1 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; EWALD/PME/PPPM parameters pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 ; Temperature and pressure coupling are off during EM tcoupl = no pcoupl = no ; No velocities during EM gen_vel = no Bond parameters continuation = no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 2 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy To use a single MPI is correct to do so: -mpirun -np 1 mdrun -s *.trp ?? There still exists the possibility of using the Point Decomposition method (mdrun -pd) in gromacs 5.x? Best regards D.V. -- 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] Invalid order for directive defaults
Dear Gromacs Users I'm trying to study a molecule (my solute) in methanol as solvent. For my solute I use Charmm27 ff, while for methanol I want to use opls/aa ff. I do this beacuse methanol is already implemented in opls force field. My .top file is: #include "charmm27.ff/forcefield.itp" #include "charmm27.ff/nor-antib.itp" #include "oplsaa.ff/forcefield.itp" #include "oplsaa.ff/methanol.itp" [ system ] ; Name nor+met [ molecules ] ; Compound#mols MET 1000 nor-antib1 But when I star groomp program I get this error: "Fatal error: Syntax error - File forcefield.itp, line 18Last line read:'[ defaults ]' Invalid order for directive defaults " I looked at the manual and in website at http://www.gromacs.org/Documentation/Errors. I can't fix the problem. Could you help me? I use gromacs 5.0.4 Best 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.
Re: [gmx-users] Methanol geometry parameters
Dear Peter Stern. Yes, I need the starting coordination for methanol, but are there specific coordinates like for spce water or tip3p water? Where can I find the files .gro or .pdb for methanol ? Dear Chaban Similar molecules have already been studied with this methanol. This Methanol is implemented in opls force field. I appreciate the time and effort you have spent sorting out that problem. D.V. 2015-12-04 8:41 GMT+01:00 Kalev Takkis <kalev.tak...@gmail.com>: > On 3 December 2015 at 20:05, Vitaly V. Chaban <vvcha...@gmail.com> wrote: > > > You, perhaps, need to care about *compatibility* of this old methanol and > > your solute molecule. > > > > > Why? General caution or do you know that there is something wrong with it? > Because if I'm not mistaken, it's the same methanol distributed with > Gromacs. > > All the best, > Kalev > > > > > > > > > > > > > On Thu, Dec 3, 2015 at 2:08 PM, Peter Stern <peter.st...@weizmann.ac.il> > > wrote: > > > > > The force field parameters are defined in ffbonded.itp and > > ffnonbonded.itp. > > > You still need starting coordinates for your molecule. > > > There are plenty of programs which will do this, but you can probably > > find > > > it in some pdb entry. > > > But, it is also trivial to do by hand since there are only two atoms > and > > > you know the C-O bond distance, e.g.: > > > HETATM1 C MOH 1 1 0.000 0.000 1.410 1.00 1.00 > > > HETATM2 O MOH 1 1 0.000 0.000 0.000 1.00 1.00 > > > > > > You should use an existing pdb or gro file as a template for the > correct > > > format. gmx pdb2gmx will add the H-atoms. > > > > > > Peter Stern > > > > > > -Original Message- > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of > Daniele > > > Veclani > > > Sent: Thursday, December 03, 2015 3:31 PM > > > To: gmx-us...@gromacs.org > > > Subject: Re: [gmx-users] Methanol geometry parameters > > > > > > Thank you for your reply. > > > > > > Yes, The .itp file for methanol comes from gromacs. But but I need the > > > .gro file. I need the geometric parameters like distances, angles and > > > diedrals. > > > these parameters are not in the .itp file or I'm wrong?? > > > > > > Best regards > > > D.V. > > > -- > > > 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. > > > > > -- > > 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. > -- 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] Methanol geometry parameters
Dear Stern. I apologize for the disruption. Create pdb file is very simple. but the distances and bond angles of methanol where I find them? I do not think can I put random distances and angles? Best D.V. 2015-12-04 12:50 GMT+01:00 Barnett, James W <jbarn...@tulane.edu>: > On Fri, 2015-12-04 at 09:43 +0100, Daniele Veclani wrote: > > Dear Peter Stern. > > > > Yes, I need the starting coordination for methanol, but are there > specific > > coordinates like for spce water or tip3p water? > > > > Where can I find the files .gro or .pdb for methanol ? > > Creating a methanol pdb file should be quick with a program like Avogadro > or > maybe AmberTool's xleap. Then use "gmx solvate" to get coordinates for > water. > > > > > > > Dear Chaban > > > > Similar molecules have already been studied with this methanol. > > > > This Methanol is implemented in opls force field. > > > > I appreciate the time and effort you have spent sorting out that problem. > > > > D.V. > > > > > > 2015-12-04 8:41 GMT+01:00 Kalev Takkis <kalev.tak...@gmail.com>: > > > > > On 3 December 2015 at 20:05, Vitaly V. Chaban <vvcha...@gmail.com> > wrote: > > > > > > > You, perhaps, need to care about *compatibility* of this old > methanol and > > > > your solute molecule. > > > > > > > > > > > > > Why? General caution or do you know that there is something wrong with > it? > > > Because if I'm not mistaken, it's the same methanol distributed with > > > Gromacs. > > > > > > All the best, > > > Kalev > > > > > > > > > > > > > > > > > > > > > > > > > > > On Thu, Dec 3, 2015 at 2:08 PM, Peter Stern < > peter.st...@weizmann.ac.il> > > > > wrote: > > > > > > > > > The force field parameters are defined in ffbonded.itp and > > > > ffnonbonded.itp. > > > > > You still need starting coordinates for your molecule. > > > > > There are plenty of programs which will do this, but you can > probably > > > > find > > > > > it in some pdb entry. > > > > > But, it is also trivial to do by hand since there are only two > atoms > > > and > > > > > you know the C-O bond distance, e.g.: > > > > > HETATM1 C MOH 1 1 0.000 0.000 1.410 1.00 1.00 > > > > > HETATM2 O MOH 1 1 0.000 0.000 0.000 1.00 1.00 > > > > > > > > > > You should use an existing pdb or gro file as a template for the > > > correct > > > > > format. gmx pdb2gmx will add the H-atoms. > > > > > > > > > > Peter Stern > > > > > > > > > > -Original Message- > > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > > > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of > > > Daniele > > > > > Veclani > > > > > Sent: Thursday, December 03, 2015 3:31 PM > > > > > To: gmx-us...@gromacs.org > > > > > Subject: Re: [gmx-users] Methanol geometry parameters > > > > > > > > > > Thank you for your reply. > > > > > > > > > > Yes, The .itp file for methanol comes from gromacs. But but I need > the > > > > > .gro file. I need the geometric parameters like distances, angles > and > > > > > diedrals. > > > > > these parameters are not in the .itp file or I'm wrong?? > > > > > > > > > > Best regards > > > > > D.V. > > > > > -- > > > > > 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_L
Re: [gmx-users] Methanol geometry parameters
Thank you for your reply. Yes, The .itp file for methanol comes from gromacs. But but I need the .gro file. I need the geometric parameters like distances, angles and diedrals. these parameters are not in the .itp file or I'm wrong?? Best regards D.V. -- 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] SDF problem
Dear gromacs user
My system consist of 1 molecule + 1000 of solvents (water) in cubic
box. I did 5 ns NPT equilibration and currently I am doing analysis stuff
such as RDF, density, viscosity, etc. And now I want to try using g_spatial
but
I stuck on it. I would like to know if you can help me in this.
In Gromacs manual, they wrote like this:
1. Use make_ndx to create a group containing the atoms around which you
want
the SDF
2. trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none
3. trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans
4. run g_spatial on the .xtc output of step #3.
5. Load grid.cube into VMD and view as an isosurface
I have tried to follow those steps but I coud not get any pretty SDF
picture
This is what I have done following the above mentioned steps:
step 1: I have my index file
step 2: I choose my molecule ("solute") as group for centering
and I select "system" (1 molecule + 1000 solvents) as an output group
step 3: Again, I choose "solute" and choose "system" as an output
step 4: I run g_spatial and select "1000 solvents" for both calculation and
output. It gives me warning to increase nab values, so I increase the nab =
100. I got grid.cube but the size of the file is not that big (the manual
says
it is around 3 copies of *.xtc file).
step 5: I load grid.cube into VMD as an isosurface. I got only a sphere of
solvents there on the VMD display
How can I view the molecule?
I use Gromacs 5.0.4.
Regards.
D.V.
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Re: [gmx-users] Invalid order for directive atomtypes
So I have to make a single .itp file with the parameters of the solute and solvent? D.V. 2015-09-21 14:58 GMT+02:00 Justin Lemkul <jalem...@vt.edu>: > > > On 9/21/15 8:53 AM, Daniele Veclani wrote: > >> Dear Justin. >> >> Thanks for you quick answer, >> >> I checked the your suggested link. >> >> But I have that both molecules (solvent and solute) introduce new atoms >> types. >> >> How can I do?? >> >> > Group them together and introduce them before any ligand [moleculetype] > appears. > > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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] Invalid order for directive atomtypes
Dear Gromacs Useres I'm trying to study a molecule in methanol (I have already studied this molecule in water) with charmm27 force field. I created the file .itp for methanol (solvent): [ atomtypes ] ; name at.num mass charge ptypesigmaepsilon CR 6 12.0110 0.0 A 0.3875410.230120 HCMM11.0079 0.0 A 0.2351970.092048 OR 8 15.9994 0.0 A 0.3153780.636386 HOR 11.0079 0.0 A 0.0400010.192464 [ pairtypes ] ; i jfunc sigma1-4 epsilon1-4 ; THESE ARE 1-4 INTERACTIONS CR CR 1 0.3385410.041840 CR HCMM 1 0.2868690.062059 CR OR 1 0.3269600.163176 CR HOR1 0.1892710.089737 [ moleculetype ] ; Name nrexcl SOL 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CR 1 SOL C 1 0.2800 12.0110 2 HCMM 1 SOL H 2 0. 1.0079 3 HCMM 1 SOL H1 3 0. 1.0079 4 HCMM 1 SOL H2 4 0. 1.0079 5 OR 1 SOL O 5 -0.6800 15.9994 6 HOR 1 SOL H3 6 0.4000 1.0079 [ bonds ] ; ai aj fu b0 kb, b0 kb 5 6 1 0.09720 469365.3 0.09720 469365.3 5 1 1 0.14180 303937.5 0.14180 303937.5 2 1 1 0.10930 287014.9 0.10930 287014.9 1 4 1 0.10930 287014.9 0.10930 287014.9 1 3 1 0.10930 287014.9 0.10930 287014.9 [ pairs ] ; ai aj fu 2 6 1 3 6 1 4 6 1 [ angles ] ; ai aj ak fu th0 kth ub0 kub th0 kth ub0 kub 2 1 3 1 108.8360 310.74108.8360 310.74 2 1 4 1 108.8360 310.74108.8360 310.74 2 1 5 1 108.5770 470.32108.5770 470.32 3 1 4 1 108.8360 310.74108.8360 310.74 3 1 5 1 108.5770 470.32108.5770 470.32 4 1 5 1 108.5770 470.32108.5770 470.32 1 5 6 1 106.5030 477.55106.5030 477.55 [ dihedrals ] ; ai aj ak al fu phi0 kphi mult phi0 kphi mult 2 1 5 6 9 0.00 1.2468 1 0.00 1.2468 1 2 1 5 6 9 180.00 -0.5774 2 180.00 -0.5774 2 2 1 5 6 9 0.00 0.7238 3 0.00 0.7238 3 3 1 5 6 9 0.00 1.2468 1 0.00 1.2468 1 3 1 5 6 9 180.00 -0.5774 2 180.00 -0.5774 2 3 1 5 6 9 0.00 0.7238 3 0.00 0.7238 3 4 1 5 6 9 0.00 1.2468 1 0.00 1.2468 1 4 1 5 6 9 180.00 -0.5774 2 180.00 -0.5774 2 4 1 5 6 9 0.00 0.7238 3 0.00 0.7238 3 [ dihedrals ] ; ai aj ak al fu xi0 kxi xi0 kxi 1 2 5 4 2 0.00 0. 0.00 0. 1 2 5 3 2 0.00 0. 0.00 0. #ifdef POSRES_LIGAND [ position_restraints ] ; atom type fx fy fz 1 1 1000 1000 1000 5 1 1000 1000 1000 #endif And I included this file in the topology file: #include "charmm27.ff/forcefield.itp" #include "charmm27.ff/nor-antib.itp" #include "charmm27.ff/metanolo.itp" [ system ] ; Name nor [ molecules ] ; Compound#mols SOL 1000 nor-antib1 when I run grompp i get this error: Fatal error: Syntax error - File metanolo.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes What am I doing wrong?? (i use gromacs 5.0.4) Best regard D.V. -- 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] Invalid order for directive atomtypes
Dear Justin. Thanks for you quick answer, I checked the your suggested link. But I have that both molecules (solvent and solute) introduce new atoms types. How can I do?? best regard D.V. 2015-09-21 14:15 GMT+02:00 Justin Lemkul <jalem...@vt.edu>: > > > On 9/21/15 8:06 AM, Daniele Veclani wrote: > >> Dear Gromacs Useres >> >> I'm trying to study a molecule in methanol (I have already studied this >> molecule in water) with charmm27 force field. >> >> I created the file .itp for methanol (solvent): >> >> [ atomtypes ] >> ; name at.num mass charge ptypesigmaepsilon >> CR 6 12.0110 0.0 A 0.3875410.230120 >> HCMM11.0079 0.0 A 0.2351970.092048 >> OR 8 15.9994 0.0 A 0.3153780.636386 >> HOR 11.0079 0.0 A 0.0400010.192464 >> >> >> [ pairtypes ] >> ; i jfunc sigma1-4 epsilon1-4 ; THESE ARE 1-4 >> INTERACTIONS >> CR CR 1 0.3385410.041840 >> CR HCMM 1 0.2868690.062059 >> CR OR 1 0.3269600.163176 >> CR HOR1 0.1892710.089737 >> >> [ moleculetype ] >> ; Name nrexcl >> SOL 3 >> >> [ atoms ] >> ; nr type resnr resid atom cgnr charge mass >> 1 CR 1 SOL C 1 0.2800 12.0110 >> 2 HCMM 1 SOL H 2 0. 1.0079 >> 3 HCMM 1 SOL H1 3 0. 1.0079 >> 4 HCMM 1 SOL H2 4 0. 1.0079 >> 5 OR 1 SOL O 5 -0.6800 15.9994 >> 6 HOR 1 SOL H3 6 0.4000 1.0079 >> >> [ bonds ] >> ; ai aj fu b0 kb, b0 kb >>5 6 1 0.09720 469365.3 0.09720 469365.3 >>5 1 1 0.14180 303937.5 0.14180 303937.5 >>2 1 1 0.10930 287014.9 0.10930 287014.9 >>1 4 1 0.10930 287014.9 0.10930 287014.9 >>1 3 1 0.10930 287014.9 0.10930 287014.9 >> >> [ pairs ] >> ; ai aj fu >>2 6 1 >>3 6 1 >>4 6 1 >> >> [ angles ] >> ; ai aj ak fu th0 kth ub0 kub th0 kth ub0 kub >>2 1 3 1 108.8360 310.74108.8360 310.74 >>2 1 4 1 108.8360 310.74108.8360 310.74 >>2 1 5 1 108.5770 470.32108.5770 470.32 >>3 1 4 1 108.8360 310.74108.8360 310.74 >>3 1 5 1 108.5770 470.32108.5770 470.32 >>4 1 5 1 108.5770 470.32108.5770 470.32 >>1 5 6 1 106.5030 477.55106.5030 477.55 >> >> [ dihedrals ] >> ; ai aj ak al fu phi0 kphi mult phi0 kphi mult >>2 1 5 6 9 0.00 1.2468 1 0.00 1.2468 1 >>2 1 5 6 9 180.00 -0.5774 2 180.00 -0.5774 2 >>2 1 5 6 9 0.00 0.7238 3 0.00 0.7238 3 >>3 1 5 6 9 0.00 1.2468 1 0.00 1.2468 1 >>3 1 5 6 9 180.00 -0.5774 2 180.00 -0.5774 2 >>3 1 5 6 9 0.00 0.7238 3 0.00 0.7238 3 >>4 1 5 6 9 0.00 1.2468 1 0.00 1.2468 1 >>4 1 5 6 9 180.00 -0.5774 2 180.00 -0.5774 2 >>4 1 5 6 9 0.00 0.7238 3 0.00 0.7238 3 >> >> [ dihedrals ] >> ; ai aj ak al fu xi0 kxi xi0 kxi >>1 2 5 4 2 0.00 0. 0.00 0. >>1 2 5 3 2 0.00 0. 0.00 0. >> >> >> #ifdef POSRES_LIGAND >> [ position_restraints ] >> ; atom type fx fy fz >> 1 1 1000 1000 1000 >> 5 1 1000 1000 1000 >> #endif >> >> >> And I included this file in the topology file: >> >> #include "charmm27.ff/forcefield.itp" >> >> #include "charmm27.ff/nor-antib.itp" >> >> #include "charmm27.ff/metanolo.itp" >> >> [ system ] >> ; Name >> nor >> >> [ molecules ] >> ; Compound#mols >> SOL 1000 >> nor-antib1 >> >> when I run grompp i get this error: >> >> Fatal error: >> Syntax error - File metanolo.itp, line 7 >> Last line read: >> '[ atomtypes ]' >> Invalid order for directive atomtypes >> >> >> What am I doing wrong?? (i use gromacs 5.0.4) >> >> > Please search the archive (I answer this question weekly) and/or visit the > GROMACS Error page, which discusses this situation/error specifically. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Science
Re: [gmx-users] No default Ryckaert-Bell. types
Dear Naga Rajesh Tummala I read in the manual the part relating to Ryckaert-Bell. angles. But I did not understand how to enter the 5 parameters. Do you tell me where I can find a guide? Best regard 2015-09-02 18:02 GMT+02:00 Naga Rajesh Tummala <nagaraj...@gatech.edu>: > In the dihedrals section, similar to the bonds and angles section, the > parameters are followed after the dihedral type.. > > 2 1 3 4 3 v0 v1 v2 v3 v4 v5 for RB type > > > > On Wed, Sep 2, 2015 at 11:48 AM, Daniele Veclani <danielevecl...@gmail.com > > > wrote: > > > Thank you for your answer. > > > > how can I put these parameters in the .top file? > > > > Best regard. > > > > > > > > 2015-09-02 17:34 GMT+02:00 Naga Rajesh Tummala <nagaraj...@gatech.edu>: > > > > > The parameters for the RB dihedral in line 227 are not described in the > > > opls forcefield. Either you can provide the parameters in your top file > > or > > > include the dihedral paramters in the opls forcefield files tht comes > > with > > > gromacs. > > > > > > > > > > > > On Wed, Sep 2, 2015 at 11:28 AM, Daniele Veclani < > > danielevecl...@gmail.com > > > > > > > wrote: > > > > > > > Dear users. > > > > > > > > > > > > I'm trying to build the file .top for a molecule with opls FF. > > > > > > > > To do this I used MKTOP but when I run grompp I get this error: > > > > > > > > "ERROR 23 [file nor.top, line 227]: > > > > No default Ryckaert-Bell. types" > > > > > > > > This is my file .top: > > > > > > > > [ moleculetype ] > > > > ; Namenrexcl > > > > MOL 3 > > > > > > > > [ atoms ] > > > > ; nr type resnr residue atom cgnr charge mass > > > > typeBchargeB massB > > > > 1 opls_268 1 MOL O11 -0.61100 15.9994 > > > > 2 opls_270 1 MOL H11 0.44100 1.008 > > > > 3 opls_267 1 MOL C11 0.81100 12.011 > > > > 4 opls_269 1 MOL O21 -0.54900 15.9994 > > > > 5 opls_141 1 MOL C22 -0.52100 12.011 > > > > 6 opls_145 1 MOL C33 0.07300 12.011 > > > > 7 opls_140 1 MOL H23 0.14200 1.008 > > > > 8 opls_280 1 MOL C44 0.62500 12.011 > > > > 9 opls_281 1 MOL O34 -578.0 15.9994 > > > >10 opls_145 1 MOL C55 -0.12600 12.011 > > > >11 opls_145B 1 MOL C66 0.13300 12.011 > > > >12 opls_145 1 MOL C77 -0.26700 12.011 > > > >13 opls_146 1 MOL H37 0.19900 1.008 > > > >14 opls_718 1 MOL C88 0.27000 12.011 > > > >15 opls_719 1 MOL F18 -0.18000 18.9984 > > > >16 opls_145 1 MOL C99 0.03900 12.011 > > > >17 opls_145 1 MOL C1010 -0.24200 12.011 > > > >18 opls_146 1 MOL H410 0.15800 1.008 > > > >19 opls_902 1 MOL N19 -0.11600 14.0067 > > > >20 opls_908 1 MOL C1111 -0.12000 12.011 > > > >21 opls_140 1 MOL H511 0.09300 1.008 > > > >22 opls_140 1 MOL H611 0.07400 1.008 > > > >23 opls_907 1 MOL C1212 0.11300 12.011 > > > >24 opls_140 1 MOL H712 0.07600 1.008 > > > >25 opls_140 1 MOL H812 0.05500 1.008 > > > >26 opls_908 1 MOL C1313 -0.12400 12.011 > > > >27 opls_140 1 MOL H913 0.07300 1.008 > > > >28 opls_140 1 MOL H1013 0.07700 1.008 > > > >29 opls_907 1 MOL C1414 0.10200 12.011 > > > >30 opls_140 1 MOL H1114 0.08500 1.008 > > > >31 opls_140 1 MOL H1214 0.05300 1.008 > > > >32 opls_901 1 MOL N212 -0.71000 14.0067 > > > >33 opls_910 1 MOL H1312 0.35700 1.008 > > > >
[gmx-users] No default Ryckaert-Bell. types
Dear users. I'm trying to build the file .top for a molecule with opls FF. To do this I used MKTOP but when I run grompp I get this error: "ERROR 23 [file nor.top, line 227]: No default Ryckaert-Bell. types" This is my file .top: [ moleculetype ] ; Namenrexcl MOL 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_268 1 MOL O11 -0.61100 15.9994 2 opls_270 1 MOL H11 0.44100 1.008 3 opls_267 1 MOL C11 0.81100 12.011 4 opls_269 1 MOL O21 -0.54900 15.9994 5 opls_141 1 MOL C22 -0.52100 12.011 6 opls_145 1 MOL C33 0.07300 12.011 7 opls_140 1 MOL H23 0.14200 1.008 8 opls_280 1 MOL C44 0.62500 12.011 9 opls_281 1 MOL O34 -578.0 15.9994 10 opls_145 1 MOL C55 -0.12600 12.011 11 opls_145B 1 MOL C66 0.13300 12.011 12 opls_145 1 MOL C77 -0.26700 12.011 13 opls_146 1 MOL H37 0.19900 1.008 14 opls_718 1 MOL C88 0.27000 12.011 15 opls_719 1 MOL F18 -0.18000 18.9984 16 opls_145 1 MOL C99 0.03900 12.011 17 opls_145 1 MOL C1010 -0.24200 12.011 18 opls_146 1 MOL H410 0.15800 1.008 19 opls_902 1 MOL N19 -0.11600 14.0067 20 opls_908 1 MOL C1111 -0.12000 12.011 21 opls_140 1 MOL H511 0.09300 1.008 22 opls_140 1 MOL H611 0.07400 1.008 23 opls_907 1 MOL C1212 0.11300 12.011 24 opls_140 1 MOL H712 0.07600 1.008 25 opls_140 1 MOL H812 0.05500 1.008 26 opls_908 1 MOL C1313 -0.12400 12.011 27 opls_140 1 MOL H913 0.07300 1.008 28 opls_140 1 MOL H1013 0.07700 1.008 29 opls_907 1 MOL C1414 0.10200 12.011 30 opls_140 1 MOL H1114 0.08500 1.008 31 opls_140 1 MOL H1214 0.05300 1.008 32 opls_901 1 MOL N212 -0.71000 14.0067 33 opls_910 1 MOL H1312 0.35700 1.008 34 opls_902 1 MOL N33 -0.11200 14.0067 35 opls_908 1 MOL C1515 0.19100 12.011 36 opls_140 1 MOL H1415 0.03700 1.008 37 opls_140 1 MOL H1515 0.0 1.008 38 opls_135 1 MOL C1616 -0.26000 12.011 39 opls_140 1 MOL H1616 0.08900 1.008 40 opls_140 1 MOL H1716 0.08000 1.008 41 opls_140 1 MOL H1816 0.07500 1.008 [ bonds ] 1 2 1 0.099 462750.4 1 3 1 0.133 376560.0 3 4 1 0.121 476976.0 3 5 1 0.150 343088.0 5 6 1 0.137 357313.6 5 8 1 0.145 343088.0 6 7 1 0.108 284512.0 6 34 1 0.135 402500.8 8 9 1 0.125 476976.0 8 10 1 0.147 334720.0 10 11 1 0.141 392459.2 10 12 1 0.141 392459.2 11 17 1 0.141 392459.2 11 34 1 0.140 20.0 12 13 1 0.108 307105.6 12 14 1 0.136 392459.2 14 15 1 0.135 351456.0 14 16 1 0.142 392459.2 16 17 1 0.140 392459.2 16 19 1 0.140 402500.8 17 18 1 0.108 307105.6 19 20 1 0.148 319657.6 19 26 1 0.146 319657.6 20 21 1 0.109 284512.0 20 22 1 0.110 284512.0 20 23 1 0.153 224262.4 23 24 1 0.109 284512.0 23 25 1 0.109 284512.0 23 32 1 0.146 319657.6 26 27 1 0.109 284512.0 26 28 1 0.111 284512.0 26 29 1 0.154 224262.4 29 30 1 0.110 284512.0 29 31 1 0.109 284512.0 29 32 1 0.146 319657.6 32 33 1 0.102 363171.2 34 35 1 0.147 319657.6 35 36 1 0.109 284512.0 35 37 1 0.109 284512.0 35 38 1 0.153 224262.4 38 39 1 0.109 284512.0 38 40 1 0.109 284512.0 38 41 1 0.109 284512.0 [ angles ] 1 3 4 1 122.613 669.440 1 3 5 1 115.207 585.760 2 1 3 1 108.493 292.880 3 5 6 1 117.303 585.760 3 5 8 1 122.815 585.760 4 3 5 1 122.180 669.440 5 6 7 1 118.516 418.400 5 6 34 1 124.720 669.440 5 8 9 1 123.231 669.440 5 8 10 1 115.012 585.760 6 5 8 1 119.879 585.760 6 34 11 1 119.618 669.440 6 34 35 1 118.344 418.400 7 6 34 1 116.763 669.440 8 10 11 1 121.987 585.760 8 10 12 1 119.361 711.280 9 8 10 1 121.756 669.440 10 11 17 1 119.731 527.184 10 11 34 1 118.777 669.440 10 12 13 1 118.733 292.880 10 12 14 1 120.570 527.184 11 10 12 1 118.650 527.184 11 17 16 1 121.908 527.184 11 17 18 1 119.847 292.880 11 34 35 1 121.996 669.440 12 14 15 1 118.664 669.440 12 14 16 1 122.613 527.184 13 12 14 1 120.674 292.880 14 16 17 1 116.514
Re: [gmx-users] No default Ryckaert-Bell. types
Thank you for your answer. how can I put these parameters in the .top file? Best regard. 2015-09-02 17:34 GMT+02:00 Naga Rajesh Tummala <nagaraj...@gatech.edu>: > The parameters for the RB dihedral in line 227 are not described in the > opls forcefield. Either you can provide the parameters in your top file or > include the dihedral paramters in the opls forcefield files tht comes with > gromacs. > > > > On Wed, Sep 2, 2015 at 11:28 AM, Daniele Veclani <danielevecl...@gmail.com > > > wrote: > > > Dear users. > > > > > > I'm trying to build the file .top for a molecule with opls FF. > > > > To do this I used MKTOP but when I run grompp I get this error: > > > > "ERROR 23 [file nor.top, line 227]: > > No default Ryckaert-Bell. types" > > > > This is my file .top: > > > > [ moleculetype ] > > ; Namenrexcl > > MOL 3 > > > > [ atoms ] > > ; nr type resnr residue atom cgnr charge mass > > typeBchargeB massB > > 1 opls_268 1 MOL O11 -0.61100 15.9994 > > 2 opls_270 1 MOL H11 0.44100 1.008 > > 3 opls_267 1 MOL C11 0.81100 12.011 > > 4 opls_269 1 MOL O21 -0.54900 15.9994 > > 5 opls_141 1 MOL C22 -0.52100 12.011 > > 6 opls_145 1 MOL C33 0.07300 12.011 > > 7 opls_140 1 MOL H23 0.14200 1.008 > > 8 opls_280 1 MOL C44 0.62500 12.011 > > 9 opls_281 1 MOL O34 -578.0 15.9994 > >10 opls_145 1 MOL C55 -0.12600 12.011 > >11 opls_145B 1 MOL C66 0.13300 12.011 > >12 opls_145 1 MOL C77 -0.26700 12.011 > >13 opls_146 1 MOL H37 0.19900 1.008 > >14 opls_718 1 MOL C88 0.27000 12.011 > >15 opls_719 1 MOL F18 -0.18000 18.9984 > >16 opls_145 1 MOL C99 0.03900 12.011 > >17 opls_145 1 MOL C1010 -0.24200 12.011 > >18 opls_146 1 MOL H410 0.15800 1.008 > >19 opls_902 1 MOL N19 -0.11600 14.0067 > >20 opls_908 1 MOL C1111 -0.12000 12.011 > >21 opls_140 1 MOL H511 0.09300 1.008 > >22 opls_140 1 MOL H611 0.07400 1.008 > >23 opls_907 1 MOL C1212 0.11300 12.011 > >24 opls_140 1 MOL H712 0.07600 1.008 > >25 opls_140 1 MOL H812 0.05500 1.008 > >26 opls_908 1 MOL C1313 -0.12400 12.011 > >27 opls_140 1 MOL H913 0.07300 1.008 > >28 opls_140 1 MOL H1013 0.07700 1.008 > >29 opls_907 1 MOL C1414 0.10200 12.011 > >30 opls_140 1 MOL H1114 0.08500 1.008 > >31 opls_140 1 MOL H1214 0.05300 1.008 > >32 opls_901 1 MOL N212 -0.71000 14.0067 > >33 opls_910 1 MOL H1312 0.35700 1.008 > >34 opls_902 1 MOL N33 -0.11200 14.0067 > >35 opls_908 1 MOL C1515 0.19100 12.011 > >36 opls_140 1 MOL H1415 0.03700 1.008 > >37 opls_140 1 MOL H1515 0.0 1.008 > >38 opls_135 1 MOL C1616 -0.26000 12.011 > >39 opls_140 1 MOL H1616 0.08900 1.008 > >40 opls_140 1 MOL H1716 0.08000 1.008 > >41 opls_140 1 MOL H1816 0.07500 1.008 > > > > > > > > > > [ bonds ] > > 1 2 1 0.099 462750.4 > > 1 3 1 0.133 376560.0 > > 3 4 1 0.121 476976.0 > > 3 5 1 0.150 343088.0 > > 5 6 1 0.137 357313.6 > > 5 8 1 0.145 343088.0 > > 6 7 1 0.108 284512.0 > > 6 34 1 0.135 402500.8 > > 8 9 1 0.125 476976.0 > > 8 10 1 0.147 334720.0 > > 10 11 1 0.141 392459.2 > > 10 12 1 0.141 392459.2 > > 11 17 1 0.141 392459.2 > > 11 34 1 0.140 20.0 > > 12 13 1 0.108 307105.6 > > 12 14 1 0.136 392459.2 > > 14 15 1 0.135 351456.0 > > 14 16 1 0.142 392459.2 > > 16 17 1 0.140 392459.2 > > 16 19 1 0.140 402500.8 > > 1
[gmx-users] solvation free energy, electrostatic transformation
I'm trying to calculate the solvation free energy of a molecule (M). I have done a VdW. transformation. I have done also a electrostatic transformation. But I get an incorrect value (large overestimation of DG solvation). I use gromacs 5.0.4 with gromos 54a7 force fields and my .mdp file (for lambda 00) is: integrator = sd tinit= 0 dt = 0.002 nsteps = 250 comm_mode= angular nstcomm = 100 nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy= 500 nstxout-compressed = 0 cutoff-scheme= group nstlist = 0 ns_type = simple pbc = no rlist= 0 coulombtype = cutoff rcoulomb = 0 epsilon_r= 1 vdwtype = cutoff rvdw = 0 DispCorr = no fourierspacing = 0.12 pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 tcoupl = berendsen tc_grps = system tau_t= 0.1 ref_t= 300 Pcoupl = no tau_p= 1.0 compressibility = 4.5e-05 ref_p= 1.0 free_energy = yes init_lambda_state= 0 delta_lambda = 0 calc_lambda_neighbors= 1 vdw_lambdas = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 coul_lambdas = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 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 restraint_lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 mass_lambdas = 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 sc-alpha = 0.5 sc-coul = no sc-power = 1.0 sc-sigma = 0.3 couple-moltype = QUI couple-lambda0 = vdw-q couple-lambda1 = vdw couple-intramol = no nstdhdl = 10 gen_vel = no constraints = all-bonds ; we only have C-H bonds here constraint-algorithm = lincs continuation = no lincs-order = 12 What's wrong? Best regards D.V. -- 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] solvation free energy, electrostatic transformation
Yes I have a experimental value. DGexp=1.99 kcal/mol DGcalc.=-14.36 kcal/mol But if I stop the VdW transformation, i get: DGonlyVdW= 2.38 and this value is in line with other data found in the literature. Thank you for your answer D.V. 2015-07-27 16:08 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 7/27/15 9:55 AM, Daniele Veclani wrote: I'm trying to calculate the solvation free energy of a molecule (M). I have done a VdW. transformation. I have done also a electrostatic transformation. But I get an incorrect value (large overestimation of DG solvation). So presumably you have an experimental value of DGsolv? How different are the values? I use gromacs 5.0.4 with gromos 54a7 force fields and my .mdp file (for lambda 00) is: integrator = sd tinit= 0 dt = 0.002 nsteps = 250 comm_mode= angular nstcomm = 100 nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy= 500 nstxout-compressed = 0 cutoff-scheme= group nstlist = 0 ns_type = simple pbc = no rlist= 0 coulombtype = cutoff rcoulomb = 0 epsilon_r= 1 vdwtype = cutoff rvdw = 0 DispCorr = no fourierspacing = 0.12 pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 tcoupl = berendsen tc_grps = system tau_t= 0.1 ref_t= 300 Pcoupl = no tau_p= 1.0 compressibility = 4.5e-05 ref_p= 1.0 free_energy = yes init_lambda_state= 0 delta_lambda = 0 calc_lambda_neighbors= 1 vdw_lambdas = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 coul_lambdas = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 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 restraint_lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 mass_lambdas = 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 sc-alpha = 0.5 sc-coul = no sc-power = 1.0 sc-sigma = 0.3 couple-moltype = QUI couple-lambda0 = vdw-q couple-lambda1 = vdw couple-intramol = no nstdhdl = 10 gen_vel = no constraints = all-bonds ; we only have C-H bonds here constraint-algorithm = lincs continuation = no lincs-order = 12 What's wrong? If you're getting a result that does not agree with a known quantity, without any errors in the run or the analysis, it means your topology for that molecule is bad and needs to be better parametrized. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] solvation free energy, electrostatic transformation
OK! I got it I created the topology with automated topology builder, and I also optimized the molecule in gaussian, and the charges are similar. Are there other ways to derive the cherges? D.V. 2015-07-27 16:30 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 7/27/15 10:28 AM, Daniele Veclani wrote: Yes I have a experimental value. DGexp=1.99 kcal/mol DGcalc.=-14.36 kcal/mol But if I stop the VdW transformation, i get: DGonlyVdW= 2.38 and this value is in line with other data found in the literature. That's only part of the transformation. Despite the fact that it looks pretty, it's not the solvation free energy. Your topology is such that the electrostatic interactions are way to favorable. You need better parameters (charges). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Create file topology in oplsaa
Dear users I'm trying to create a topology file for a molecule to oplsaa force fields How can I do this? I have read that I can do this with the program MKTOP but I can not use it. Is there a tutorial for this program? Best regards Daniele. -- 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] solvation free energy
OK! I got it. I have to put: couple-intramol = yes but I have to define couple-lambda 0 and couple-lamba-1? how do I turn off the 1-4 pair interaction? 2015-07-17 13:32 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 7/17/15 6:34 AM, Daniele Veclani wrote: I read the manual and also some examples of free energy calculation. when I do the simulation: M(vacuo) -- nothing(vacuo) I leave only intramolecular interactions. How can I just leave these interactions? I don't find the answer in the manual. couple-intramol = no does not subject intramolecular interactions to lambda coupling. But doing this in vacuo is pointless, because then by definition, nothing changes. -Justin Best regards D.V. 2015-07-17 10:10 GMT+02:00 hannes.loeff...@stfc.ac.uk: I do not know how your top file looks like and what you have done to it. The setup procedure to create the topolog file would be as for a standard MD simulation with M. You would make sure that the QUI label referes to the right indexes in your index file and run TI with you preferred protocol. This simplified setup procedure ensures that you do not have to modify the topology file in any way esp. not to have to set up an explicit B state. I suggest to read all parts relating to couple-* in the manual. This is scattered over several places in the text. Cheers, Hannes. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Daniele Veclani [danielevecl...@gmail.com] Sent: 17 July 2015 08:57 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] solvation free energy Thank you for your answer. I read the manual. As I understand it, I should be deleted, from .top file, the section of non-bonded parameters. It's right? Of course, after the VdW I'll change the electrostatic transformation. Best regards D.V. 2015-07-16 16:55 GMT+02:00 Hannes Loeffler hannes.loeff...@stfc.ac.uk: The couple-* parameters take already care of including the non-bonded terms internal to your molecule to correctly describe the transfer of M to vacuum. That's the point of those parameters so that you would not have to run an additional correction in vacuo. See the discussion in the manual (it's section 5.3 for Gromacs 4.6.x). You would also need to compute the electrostatic transformation. On Thu, 16 Jul 2015 16:26:44 +0200 Daniele Veclani danielevecl...@gmail.com wrote: I'm trying to calculate the solvation free energy of a molecule (M). I have done: M+water --- dum+water Now I have to do: M(vacuo) -- dum(vacuo) In this case I have a problem, in fact I find a DG = 0.0 and within the .xvg file there are only zeros. Where is the problem? I use gromacs 5.0.4 and my .mdp file (for lambda 00) is: integrator = sd tinit= 0 dt = 0.002 nsteps = 250 comm_mode= angular nstcomm = 100 nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy= 500 nstxout-compressed = 0 cutoff-scheme= group nstlist = 0 ns_type = simple pbc = no rlist= 0 coulombtype = cutoff rcoulomb = 0 epsilon_r= 1 vdwtype = cutoff rvdw = 0 DispCorr = no fourierspacing = 0.12 pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 tcoupl = berendsen tc_grps = system tau_t= 0.1 ref_t= 300 Pcoupl = no tau_p= 1.0 compressibility = 4.5e-05 ref_p= 1.0 free_energy = yes init_lambda_state= 0 delta_lambda = 0 calc_lambda_neighbors= 1 vdw_lambdas = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00 coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 bonded_lambdas = 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 mass_lambdas = 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 sc-alpha = 0.5 sc-coul = no sc-power = 1.0 sc-sigma = 0.3 couple-moltype = QUI couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no nstdhdl = 10 gen_vel = no constraints = all-bonds ; we only have C-H bonds
Re: [gmx-users] solvation free energy
I'm using gromacs version 5.0.4, so should I upgrade to version 5.0.5 ? I read in the manual (section 5.3.4) that can turn off the 1-4 interactions without ever touching the topology, by using the couple-moltype, couple-lambda0, couple-lambda 1, and couple-intramol keywords. Can I do this? Best regards D.V. 2015-07-17 13:55 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 7/17/15 7:44 AM, Daniele Veclani wrote: OK! I got it. I have to put: couple-intramol = yes but I have to define couple-lambda 0 and couple-lamba-1? Yes, you have to tell mdrun what you're transforming. how do I turn off the 1-4 pair interaction? That requires explicit use of [pairs_nb], as I recall. There was a bug fix for that recently, so make sure you're using version 5.0.5. -Justin 2015-07-17 13:32 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 7/17/15 6:34 AM, Daniele Veclani wrote: I read the manual and also some examples of free energy calculation. when I do the simulation: M(vacuo) -- nothing(vacuo) I leave only intramolecular interactions. How can I just leave these interactions? I don't find the answer in the manual. couple-intramol = no does not subject intramolecular interactions to lambda coupling. But doing this in vacuo is pointless, because then by definition, nothing changes. -Justin Best regards D.V. 2015-07-17 10:10 GMT+02:00 hannes.loeff...@stfc.ac.uk: I do not know how your top file looks like and what you have done to it. The setup procedure to create the topolog file would be as for a standard MD simulation with M. You would make sure that the QUI label referes to the right indexes in your index file and run TI with you preferred protocol. This simplified setup procedure ensures that you do not have to modify the topology file in any way esp. not to have to set up an explicit B state. I suggest to read all parts relating to couple-* in the manual. This is scattered over several places in the text. Cheers, Hannes. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Daniele Veclani [danielevecl...@gmail.com] Sent: 17 July 2015 08:57 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] solvation free energy Thank you for your answer. I read the manual. As I understand it, I should be deleted, from .top file, the section of non-bonded parameters. It's right? Of course, after the VdW I'll change the electrostatic transformation. Best regards D.V. 2015-07-16 16:55 GMT+02:00 Hannes Loeffler hannes.loeff...@stfc.ac.uk : The couple-* parameters take already care of including the non-bonded terms internal to your molecule to correctly describe the transfer of M to vacuum. That's the point of those parameters so that you would not have to run an additional correction in vacuo. See the discussion in the manual (it's section 5.3 for Gromacs 4.6.x). You would also need to compute the electrostatic transformation. On Thu, 16 Jul 2015 16:26:44 +0200 Daniele Veclani danielevecl...@gmail.com wrote: I'm trying to calculate the solvation free energy of a molecule (M). I have done: M+water --- dum+water Now I have to do: M(vacuo) -- dum(vacuo) In this case I have a problem, in fact I find a DG = 0.0 and within the .xvg file there are only zeros. Where is the problem? I use gromacs 5.0.4 and my .mdp file (for lambda 00) is: integrator = sd tinit= 0 dt = 0.002 nsteps = 250 comm_mode= angular nstcomm = 100 nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy= 500 nstxout-compressed = 0 cutoff-scheme= group nstlist = 0 ns_type = simple pbc = no rlist= 0 coulombtype = cutoff rcoulomb = 0 epsilon_r= 1 vdwtype = cutoff rvdw = 0 DispCorr = no fourierspacing = 0.12 pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 tcoupl = berendsen tc_grps = system tau_t= 0.1 ref_t= 300 Pcoupl = no tau_p= 1.0 compressibility = 4.5e-05 ref_p= 1.0 free_energy = yes init_lambda_state= 0 delta_lambda = 0 calc_lambda_neighbors= 1 vdw_lambdas = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00 coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Re: [gmx-users] solvation free energy
Thank you for your answer. I read the manual. As I understand it, I should be deleted, from .top file, the section of non-bonded parameters. It's right? Of course, after the VdW I'll change the electrostatic transformation. Best regards D.V. 2015-07-16 16:55 GMT+02:00 Hannes Loeffler hannes.loeff...@stfc.ac.uk: The couple-* parameters take already care of including the non-bonded terms internal to your molecule to correctly describe the transfer of M to vacuum. That's the point of those parameters so that you would not have to run an additional correction in vacuo. See the discussion in the manual (it's section 5.3 for Gromacs 4.6.x). You would also need to compute the electrostatic transformation. On Thu, 16 Jul 2015 16:26:44 +0200 Daniele Veclani danielevecl...@gmail.com wrote: I'm trying to calculate the solvation free energy of a molecule (M). I have done: M+water --- dum+water Now I have to do: M(vacuo) -- dum(vacuo) In this case I have a problem, in fact I find a DG = 0.0 and within the .xvg file there are only zeros. Where is the problem? I use gromacs 5.0.4 and my .mdp file (for lambda 00) is: integrator = sd tinit= 0 dt = 0.002 nsteps = 250 comm_mode= angular nstcomm = 100 nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy= 500 nstxout-compressed = 0 cutoff-scheme= group nstlist = 0 ns_type = simple pbc = no rlist= 0 coulombtype = cutoff rcoulomb = 0 epsilon_r= 1 vdwtype = cutoff rvdw = 0 DispCorr = no fourierspacing = 0.12 pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 tcoupl = berendsen tc_grps = system tau_t= 0.1 ref_t= 300 Pcoupl = no tau_p= 1.0 compressibility = 4.5e-05 ref_p= 1.0 free_energy = yes init_lambda_state= 0 delta_lambda = 0 calc_lambda_neighbors= 1 vdw_lambdas = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00 coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 bonded_lambdas = 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 mass_lambdas = 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 sc-alpha = 0.5 sc-coul = no sc-power = 1.0 sc-sigma = 0.3 couple-moltype = QUI couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no nstdhdl = 10 gen_vel = no constraints = all-bonds ; we only have C-H bonds here constraint-algorithm = lincs continuation = no lincs-order = 12 Best regards Daniele Veclani. -- 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] solvation free energy
Then as I had already calculated the free energy in a box with solute and solvent with the option couple-intramol = no, I already have the solvatation free energy correct, Is it right?? D.V. 2015-07-17 18:10 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 7/17/15 12:08 PM, Justin Lemkul wrote: On 7/17/15 12:06 PM, David van der Spoel wrote: On 17/07/15 17:55, Justin Lemkul wrote: On 7/17/15 11:29 AM, Daniele Veclani wrote: I'm using gromacs version 5.0.4, so should I upgrade to version 5.0.5 ? If you need [ pairs_nb ], yes. But I actually don't think you do. See below. I read in the manual (section 5.3.4) that can turn off the 1-4 interactions without ever touching the topology, by using the couple-moltype, couple-lambda0, couple-lambda 1, and couple-intramol keywords. I think you're reading this section backwards. Admittedly, it's a confusing section, so let's simplify. If you turn off the nonbonded interactions of some molecule in water, the total contribution to the free energy change is composed of the solute-solute terms and solute-water terms. To get the actual solvation free energy, one needs to correct for the solute-solute terms being turned off, which is the purpose of the gas-phase simulations. Turning off interactions in vacuo tells you how much of the free energy change is attributed to intramolecular terms. The difference between the two transformations is then the solvation free energy. But, several years ago, this procedure became much easier in GROMACS with the introduction of the couple-intramol keyword. It *eliminates* the need for any gas-phase simulations or topology hacking. This is what the manual is trying to tell you. If you run your transformations in water with couple-intramol = no, then the intramolecular interactions are always full strength, so the free energy difference you calculate is solely attributed to solute-water interactions, viz. the solvation free energy. If you *want* to make your life more difficult, set couple-intramol = yes and conduct gas-phase calculations, as well, which is what requires topology hacking. I wouldn't do this. Not only is the manual somewhat unclear, but any time you have to manually modify the topology, there is a potential for error. The free energy code attempts to make your life easy and efficient, unless you have some very complex protocol to do that requires lots of work. A solvation energy is not one of these cases; it is straightforward with appropriate use of the .mdp keywords. If I understand that correctly then the protocol ignores the difference in intramolecular energy between gas-phase and solvation. This is probably OK for small and rigid molecules but not necessarily for larger or flexible molecules. When using polarizable force fields it will probably induce a significant error. Have you tried this yet? We have not done a comparison. In CHARMM, we always explicitly do gas phase, but that is by necessity. We don't have an analogous couple-intramol-style behavior. It could probably be done, but we have an established protocol that has been used for years that is rock solid. I would also agree that there would be massive errors for a polarizable force field in this case due to environmental response. I assume, for now, most people are using additive models. In fact, until I have actually tested the free energy code with our Drude model, it is explicitly disabled by grompp. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] solvation free energy
I'm trying to calculate the solvation free energy of a molecule (M). I have done: M+water --- dum+water Now I have to do: M(vacuo) -- dum(vacuo) In this case I have a problem, in fact I find a DG = 0.0 and within the .xvg file there are only zeros. Where is the problem? I use gromacs 5.0.4 and my .mdp file (for lambda 00) is: integrator = sd tinit= 0 dt = 0.002 nsteps = 250 comm_mode= angular nstcomm = 100 nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy= 500 nstxout-compressed = 0 cutoff-scheme= group nstlist = 0 ns_type = simple pbc = no rlist= 0 coulombtype = cutoff rcoulomb = 0 epsilon_r= 1 vdwtype = cutoff rvdw = 0 DispCorr = no fourierspacing = 0.12 pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 tcoupl = berendsen tc_grps = system tau_t= 0.1 ref_t= 300 Pcoupl = no tau_p= 1.0 compressibility = 4.5e-05 ref_p= 1.0 free_energy = yes init_lambda_state= 0 delta_lambda = 0 calc_lambda_neighbors= 1 vdw_lambdas = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00 coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 bonded_lambdas = 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 mass_lambdas = 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 sc-alpha = 0.5 sc-coul = no sc-power = 1.0 sc-sigma = 0.3 couple-moltype = QUI couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no nstdhdl = 10 gen_vel = no constraints = all-bonds ; we only have C-H bonds here constraint-algorithm = lincs continuation = no lincs-order = 12 Best regards Daniele Veclani. -- 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] free energy binding problem
everything, in this case only vdW couple-intramol = no nstdhdl = 10 ; Do not generate velocities gen_vel = no ; options for bonds constraints = h-bonds ; we only have C-H bonds here ; Type of constraint algorithm constraint-algorithm = lincs ; Constrain the starting configuration ; since we are continuing from NPT continuation = yes ; Highest order in the expansion of the constraint coupling matrix lincs-order = 12 Is it a symptom of poor stability of the system (not good energy minimization, or not good nvt npt)? Best regards Daniele Veclani -- 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] free energy binding
Dear A. Lemkul I'm writing about the problem with the calculation of free energy binding. I used 20 steps for the calculation of the free energy, only three of these steps (7,12,19) I find this error. And in these steps simulation terminates prematurely. Best 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] free energy binding
Dear A. Lemkul I'm writing about the problem with the calculation of free energy binding. I used 20 steps for the calculation of the free energy, only three of these steps (7,12,19) I find this error. And in these steps simulation terminates prematurely. Best 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] add. residue in topology database
Dear users I'm trying to build the topology files for a box with 1000 molecules of water and an organic molecule. when I use pdb2gmx come out the error: OUB7 not found in residue topology database how do I put this residue in the database? I have a .itp file for this molecule. I use gromacs 5.0.4. Best 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] check for bad contacts and/or reduce the time step if appropriate
Dear Gromacs Users, I am trying to simulate a box with 1000 waters. The box size are of 31,07625 A per side. When I go to do the dynamic simulation (mdrun -s 1000w.tpr -c 1000w_1.gro, I use force field opls-aa) comes out this error message: step: XX: Water molecule starting at atom xxx can not be settled check for bad contacts and/or reduce the time step if appropriate Wrote pdb files with previous and current coordinates my .mdp file is: ; 7.3.3 Run Control integrator = steep nsteps = 5 ; 7.3.5 Energy Minimization emtol = 1000 emstep = 0.001 ; 7.3.8 Output Control nstxout= 100 nstvout= 100 nstfout = 100 nstlog = 1 nstenergy = 1 energygrps = System ; 7.3.9 Neighbor Searching cutoff-scheme = Verlet verlet-buffer-tolerance = 0.005 nstlist = 10 ns_type = grid pbc= xyz rlist = 1.2 ; 7.3.10 Electrostatics coulombtype = PME rcoulomb = 1.2 ; 7.3.11 VdW vdwtype= cut-off rvdw = 1.2 DispCorr = Ener ; 7.3.13 Ewald fourierspacing = 0.12 pme_order= 4 ewald_rtol = 1e-5 can anyone please let me know what is wrong with my system Best regards Daniele Veclani -- 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.
