Re: [gmx-users] Hydrogens of ATB ligand show obvious vibration under all-bonds contraints?

[Du, Yu]

Dear GMX-Users,

The vibration of the hydrogens of methyl and methylene groups was the result of 
Trajectory Smoothing in VMD, not the problem of GROMACS's all-bond constraints.

Sorry for this distracting question.

Yu


> -Original Messages-
> From: "Du, Yu" 
> Sent Time: 2019-10-18 08:20:10 (Friday)
> To: gmx-us...@gromacs.org
> Cc: 
> Subject: Re: Re: [gmx-users] Hydrogens of ATB ligand show obvious vibration 
> under all-bonds contraints?
> 
> Hi Justin, 
> 
> Thanks for your reply.
> I will use the united-atom topology of the ligand.
> 
> Yu
> 
> 
> > -Original Messages-
> > From: "Justin Lemkul" 
> > Sent Time: 2019-10-17 23:17:47 (Thursday)
> > To: gmx-us...@gromacs.org
> > Cc: 
> > Subject: Re: [gmx-users] Hydrogens of ATB ligand show obvious vibration 
> > under all-bonds contraints?
> > 
> > 
> > 
> > On 10/17/19 11:02 AM, Du, Yu wrote:
> > > Dear GMX-Users,
> > >
> > > I'm using GMX2018.3 simulating Melatonin (ATB Link: 
> > > https://atb.uq.edu.au/molecule.py?molid=355098).
> > >
> > >
> > > I found that the hydrogens of two methyl groups (CH3, i.e. CH11, CH12, 
> > > CH13, CH14, CH15 and CH16) showed
> > > obvious vibration under the following mdp configuration:
> > >
> > >
> > > integrator  = md
> > > dt   = 0.002
> > > cutoff-scheme= group
> > > constraints = all-bonds
> > > constraint_algorithm = lincs
> > > continuation  = yes
> > >
> > >
> > > I used the gromos54a7_atb.ff.
> > >
> > >
> > >
> > >
> > > P.S. The partial topology of Melatonin from ATB
> > 
> > You're using the wrong topology. GROMOS parameter sets are united-atom, 
> > but you've chosen the all-atom topology (no idea why this exists, 
> > honestly). Your CH3 and CH2 groups should have no explicit H atoms.
> > 
> > -Justin
> > 
> > > [ moleculetype ]
> > > ; Name   nrexcl
> > > ESV6 3
> > > [ atoms ]
> > > ;  nr  type  resnr  resid  atom  cgnr  chargemass
> > >  1HC1ESV6H1610.067   1.0080
> > >  2  CPos1ESV6C1320.010  12.0110
> > >  3HC1ESV6H1430.067   1.0080
> > >  4HC1ESV6H1540.067   1.0080
> > >  5OE1ESV6 O15   -0.368  15.9994
> > >  6  CAro1ESV6 C960.398  12.0110
> > >  7  CAro1ESV6 C77   -0.385  12.0110
> > >  8HC1ESV6 H780.163   1.0080
> > >  9  CAro1ESV6 C290.085  12.0110
> > > 10  CAro1ESV6 C1   10   -0.057  12.0110
> > > 11  CAro1ESV6 C5   11   -0.144  12.0110
> > > 12HC1ESV6 H3   120.186   1.0080
> > > 13  NOpt1ESV6 N1   13   -0.354  14.0067
> > > 14  HS141ESV6 H6   140.373   1.0080
> > > 15  CAro1ESV6 C4   150.070  12.0110
> > > 16  CAro1ESV6 C8   16   -0.145  12.0110
> > > 17HC1ESV6 H8   170.156   1.0080
> > > 18  CAro1ESV6C10   18   -0.360  12.0110
> > > 19HC1ESV6 H9   190.169   1.0080
> > > 20 C1ESV6 C3   20   -0.159  12.0110
> > > 21HC1ESV6 H1   210.070   1.0080
> > > 22HC1ESV6 H2   220.070   1.0080
> > > 23  CPos1ESV6 C6   230.231  12.0110
> > > 24HC1ESV6 H4   240.014   1.0080
> > > 25HC1ESV6 H5   250.014   1.0080
> > > 26 N1ESV6 N2   26   -0.525  14.0067
> > > 27  HS141ESV6H10   270.307   1.0080
> > > 28  CPos1ESV6C11   280.684  12.0110
> > > 29 OEOpt1ESV6 O2   29   -0.616  15.9994
> > > 30 C1ESV6C12   30   -0.586  12.0110
> > > 31HC1ESV6H11   310.166   1.0080
> > > 32HC1ESV6H12   320.166   1.0080
> > > 33HC1ESV6H13   330.166   1.0080
> > > ; total charge of the molecule:   0.000
> > > [ bonds ]
> > > ;  ai   aj  funct   c0 c1
> > >  122   0.1090   1.2300e+07
> > >  232   0.1090   1.2300e+07
> > >  242   0.1090   1.2300e+07
> > >  252   0.1430   8.1800e+06
> > >  562   0.1380   4.4633e+06
> > >  672   0.1390   8.6600e+06
> > >  6   182   0.1420   3.2236e+06
> > >  782   0.1090   1.2300e+07
> > >  792   0.1410   6.5389e+06
> > >  9   102   0.1435   6.1000e+06
> > >  9   152   0.1430   8.1800e+06
> > > 10   112   0.1380   1.1000e+07
> > > 10   202   0.1500   8.3700e+06
> > > 11   122   0.1090   1.2300e+07
> > > 11   132   0.1380   1.1000e+07
> > > 13   142   0.1010   6.3719e+06
> > > 13   152   0.1380   1.1000e+07
> > > 15   162   0.1400   8.5400e+06
> > > 16   172   0.1090   1.2300e+07
> > > 16   182   0.1390   8.6600e+06
> > > 18   192   0.1090  

[gmx-users] Coarse-grained MD

[Shan Jayasinghe]

Dear Gromacs Users,

I have surfactant and triglyceride united atom models which I used to do MD
simulations with Gromacs. Now I want to do coarse grained MD simulations
for the same systems using Gromacs. Appreciate, if anyone can guide me to
setup the coarse grained simulation.

Thank you.
-- 
Best Regards
Shan Jayasinghe
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Re: [gmx-users] Question about default auto setting of mdrun -pin

[Szilárd Páll]

On Fri, Oct 18, 2019 at 4:36 PM  wrote:

> On Thu, Oct 17, 2019 at 10:34:39AM +, Kutzner, Carsten wrote:
> >
> > is it intended that the thread-MPI version of mdrun 2018 does pin to its
> core
> > if started with -nt 1 -pin auto?
>

No, I don't think that's intended.


>
> I think I have a (partial) idea about what's happening.
> get_thread_affinity_layout() performs various checks to determin if
> pinning is possible, and for -pin auto, it looks at the number of
> mdrun threads vs hardware threads. However, the number of mdrun
> threads ultimately comes from gmx_omp_nthreads_get().
> Of course, if OMP_NUM_THREADS is unset, OpenMP will default to the
> whole machine, and the above check will always succeed. And sure
> enough, setting OMP_NUM_THREADS to 1 will turn off pinning in our test
> case.
>

The source of total number of hardware threads should not be OpenMP but a
system call or hwloc -- which should (and was IIRC a while ago at least)
checked agianst the  gmx_omp_nthreads_get() value.

If however the behavior you describe is actually reproducible, please do
file a bug report.

--
Szilárd


>
> A.
>
> --
> Ansgar Esztermann
> Sysadmin Dep. Theoretical and Computational Biophysics
> http://www.mpibpc.mpg.de/grubmueller/esztermann
> --
> Gromacs Users mailing list
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[gmx-users] Question about default auto setting of mdrun -pin

[aeszter]

On Thu, Oct 17, 2019 at 10:34:39AM +, Kutzner, Carsten wrote:
> 
> is it intended that the thread-MPI version of mdrun 2018 does pin to its core
> if started with -nt 1 -pin auto?

I think I have a (partial) idea about what's happening.
get_thread_affinity_layout() performs various checks to determin if
pinning is possible, and for -pin auto, it looks at the number of
mdrun threads vs hardware threads. However, the number of mdrun
threads ultimately comes from gmx_omp_nthreads_get().
Of course, if OMP_NUM_THREADS is unset, OpenMP will default to the
whole machine, and the above check will always succeed. And sure
enough, setting OMP_NUM_THREADS to 1 will turn off pinning in our test
case.

A.

-- 
Ansgar Esztermann
Sysadmin Dep. Theoretical and Computational Biophysics
http://www.mpibpc.mpg.de/grubmueller/esztermann
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Re: [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

[Amit Jaiswal]

Dear Jorden, Many thanks for your reply. I have mentioned the files below for you to have a look. Once again thanks for your time. NVT.mdp:title = Protein-ligand complex NVT equilibrationdefine = -DPOSRES -DPOSRES_LIG ; position restrain the protein and ligand; Run parametersintegrator = md ; leap-frog integratornsteps = 3 ; 2 * 5 = 100 psdt = 0.002 ; 2 fs; Output controlnstenergy = 500 ; save energies every 1.0 psnstlog = 500 ; update log file every 1.0 ps #includenstxout-compressed = 500 ; save coordinates every 1.0 ps; Bond parameterscontinuation = no ; first dynamics runconstraint_algorithm = lincs ; holonomic constraintsconstraints = h-bonds ; bonds to H are constrainedlincs_iter = 1 ; accuracy of LINCSlincs_order = 4 ; also related to accuracy; Neighbor searching and vdWcutoff-scheme = Verletns_type = grid ; search neighboring grid cellsnstlist = 20 ; largely irrelevant with Verletrlist = 1.2vdwtype = cutoffvdw-modifier = force-switchrvdw-switch = 1.0rvdw = 1.2 ; short-range van der Waals cutoff (in nm); Electrostaticscoulombtype = PME ; Particle Mesh Ewald for long-range electrostaticsrcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)pme_order = 4 ; cubic interpolationfourierspacing = 0.16 ; grid spacing for FFT; Temperature couplingtcoupl = V-rescale ; modified Berendsen thermostattc-grps = Protein_NAD Water_and_ions ; two coupling groups - more accuratetau_t = 0.1 0.1 ; time constant, in psref_t = 300 300 ; reference temperature, one for each group, in K; Pressure couplingpcoupl = no ; no pressure coupling in NVT; Periodic boundary conditionspbc = xyz ; 3-D PBC; Dispersion correction is not used for proteins with the C36 additive FFDispCorr = no; Velocity generationgen_vel = yes ; assign velocities from Maxwell distributiongen_temp = 300 ; temperature for Maxwell distributiongen_seed = -1 ; generate a random seed posre_zn.itp:; position restraints for ZN of Gromacs Runs One Microsecond At Cannonball Speeds [ position_restraints ]; i funct fcx fcy fcz2220 1 1000 1000 1000 posre_nad.itp:; position restraints for System_H* of GRowing Old MAkes el Chrono Sweat [ position_restraints ]; i funct fcx fcy fcz1 1 1000 1000 10002 1 1000 1000 10003 1 1000 1000 10004 1 1000 1000 10005 1 1000 1000 10006 1 1000 1000 10007 1 1000 1000 10008 1 1000 1000 10009 1 1000 1000 100010 1 1000 1000 100011 1 1000 1000 100012 1 1000 1000 100013 1 1000 1000 100014 1 1000 1000 100015 1 1000 1000 100016 1 1000 1000 100017 1 1000 1000 100018 1 1000 1000 100019 1 1000 1000 100020 1 1000 1000 100021 1 1000 1000 100022 1 1000 1000 100023 1 1000 1000 100024 1 1000 1000 100025 1 1000 1000 100026 1 1000 1000 100027 1 1000 1000 100028 1 1000 1000 100029 1 1000 1000 100030 1 1000 1000 100031 1 1000 1000 100032 1 1000 1000 100033 1 1000 1000 100034 1 1000 1000 100035 1 1000 1000 100036 1 1000 1000 100037 1 1000 1000 100038 1 1000 1000 100039 1 1000 1000 100040 1 1000 1000 100041 1 1000 1000 100042 1 1000 1000 100043 1 1000 1000 100044 1 1000 1000 100045 1 1000 1000 100046 1 1000 1000 100047 1 1000 1000 100048 1 1000 1000 100049 1 1000 1000 100050 1 1000 1000 100051 1 1000 1000 100052 1 1000 1000 100053 1 1000 1000 100054 1 1000 1000 100055 1 1000 1000 100056 1 1000 1000 100057 1 1000 1000 100058 1 1000 1000 100059 1 1000 1000 100060 1 1000 1000 100061 1 1000 1000 100062 1 1000 1000 100063 1 1000 1000 100064 1 1000 1000 100065 1 1000 1000 100066 1 1000 1000 100067 1 1000 1000 100068 1 1000 1000 100069 1 1000 1000 100070 1 1000 1000 1000   Regards,Amit  15.10.2019, 09:54, "Jorden Cabal" :Dear Amit,During equilibration you add positional restraint for protein, notice thatyou have added positional restraint for Zn ion, nad and protein. It shouldnot happen if you have taken the default values while generating thepositional restraints in gromacs. However I would like to look to your"nvt.mdp", "posre_zn.itp" and "posre_nad.itp" files, in order to commenton it.Thank youOn Sat, Oct 12, 2019 at 1:50 PM Amit Jaiswal  wrote:  Dear Jorden, Many thanks for your suggestions. I solved the index file problem as I created two groups namely Protein_Zn_NAD and the other being Na_Water. But when i ran NVT equilibration, the Zn ion again got displaced far away from its original position. I cannot figure out how can i constrain the Zn ion? I guess something is wrong in the topology file. I have included the last few lines of my topology file. Please have a look whenever you are free and correct me if something is mistakenly wrong. Thanks for your time and help. *; Include Position restraint file* *#ifdef POSRES* *#include "posre.itp"* *#endif* *; Include Position restraint file* *#ifdef POSRES* *#include "posre_zn.itp"* *#endif* *; Include ligand topology* *#include "nad.itp"* *; Ligand position restraints* *#ifdef POSRES_LIG* *#include "posre_nad.itp"* *#endif* *; Include water topology* *#include "./charmm36-mar2019.ff/tip3p.itp"* *#ifdef POSRES_WATER* *; Position restraint for each water oxygen* *[ position_restraints 

[gmx-users] Fatal error: no domain decomposition

[Patricia Saenz Méndez]

Hi!
I am trying to run a simple MD simulation as usual, but with this system I
have got the same error message:






*Fatal error:There is no domain decomposition for 160 ranks that is
compatible with thegiven box and a minimum cell size of 1.02425 nmChange
the number of ranks or mdrun option -rcon or -dds or your LINCSsettingsLook
in the log file for details on the domain decomposition*

And when looking in the log file

















*Initializing Domain Decomposition on 200 ranksDynamic load balancing:
lockedMinimum cell size due to atom displacement: 0.476 nmInitial maximum
distances in bonded interactions:two-body bonded interactions: 0.431
nm, LJ-14, atoms 1820 1827  multi-body bonded interactions: 0.431 nm,
Proper Dih., atoms 1820 1827Minimum cell size due to bonded interactions:
0.474 nmMaximum distance for 5 constraints, at 120 deg. angles, all-trans:
0.819 nmEstimated maximum distance required for P-LINCS: 0.819 nmThis
distance will limit the DD cell size, you can override this with -rconGuess
for relative PME load: 0.18Will use 160 particle-particle and 40 PME only
ranksThis is a guess, check the performance at the end of the log fileUsing
40 separate PME ranks, as guessed by mdrunScaling the initial minimum size
with 1/0.8 (option -dds) = 1.25Optimizing the DD grid for 160 cells with a
minimum initial size of 1.024 nmThe maximum allowed number of cells is: X 7
Y 7 Z 7*

Those atoms are parte of a Met residue.
I have no clue how to solve this or what I am having this problem.
Thank you very much.
Cheers,

/P
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Re: [gmx-users] shift in trajectory

[Amin Rouy]

Dear Justin,

Yes, they form a clear phase separation.
Well, I did not clearly understand your last suggestion. I do not need to
have their COM coordinate, I need COM of 'A' stays in the middle of the
box.

On Thu, Oct 17, 2019 at 5:17 PM Justin Lemkul  wrote:

>
>
> On 10/17/19 8:04 AM, Amin Rouy wrote:
> > Dear Justin,
> >
> > I have a two-component system (they demix), which are grouped as  'A' and
> > 'B' from beginning of the simulation. Now my trajectory is asymmetric
> with
> > respect to the center. I can make it symmetric with gmx trjconv flag
> -shift
> > manually, but I need to apply the flag -center to get the 'A' component
> > sitting exactly at the center of the box.
> >
> > So having my index file, what I do is:
> >
> > 1- *gmx trjconv -f NPT.xtc -o NPT-centered.xtc -pbc none -n index.ndx*
> >
> > and I select whole system.
>
> Making molecules whole should always be the first step. I disagree with
> the previous advice you were given to use this PBC option first.
>
> >
> > 2- *gmx trjconv -f NPT-centered.xtc -o NPT-centered2.xtc -n index.ndx
> > -center*
> >
> > and I select group 'A' for Select group for centering, and whole system
> for
> > Select group for output.
> >
> > 3- *gmx trjconv -f NPT-centered2.xtc -o NPT-centered3.xtc -n index.ndx
> -pbc
> > mol -s NPT.tpr *
> >
> > and here I select whole system.
> >
> >
> > What I get is the same trajectory as I had in the beginning, no change at
> > all. I can see it with vitalizing and moreover from gmx density outcome.
>
> Do you get a clear phase separation with a layer of A and a layer of B
> in the simulation? In steps prior to separation, it will not be apparent
> that the molecules are actually centered, but you can obtain their COM
> coordinates with gmx traj -ox -com and confirm that they correspond to
> the box center.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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