[gmx-users] gromacs.org_gmx-users Digest, Vol 175, Issue 28 - start the simulation of the last stopping point.
Mark Abraham
mark.j.abraham at gmail.com
Wed Nov 14 05:45:34 CET 2018
Hi,
Those were not the commands you issued. What commands did you issue?
Mark
On Fri, Nov 9, 2018 at 7:12 AM Edjan Silva <edjan.silva at esenfar.ufal.br>
wrote:
> Dear Paul,
>
> Thank you for your help. However, when you run the command:
>
> $ gmx convert-tpr -s previous.tpr -extend timetoextendby -o next.tpr
> $ gmx mdrun -s next.tpr -cpi state.cpt
>
> the following error appeared:
>
>
> *Output file appending has been requested,*
> *but some output files listed in the checkpoint file md_0_1.cpt*
> *are not present or not named as the output files by the current program:*
> *Expect output files present:*
>
> *Expected output files not present or named differently:*
> * md_0_1.log*
> * md_0_1.xtc*
> * md_0_1.edr*
>
> *-------------------------------------------------------*
> *Program: gmx mdrun, version 2016.4*
> *Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 177)*
>
> *Fatal error:*
> *File appending requested, but 3 of the 3 output files are not present or
> are*
> *named differently. For safety reasons, GROMACS-2016 and later only allows
> file*
> *appending to be used when all files have the same names as they had in
> the*
> *original run. Checkpointing is merely intended for plain continuation of
> runs.*
> *For safety reasons you must specify all file names (e.g. with -deffnm),
> and*
> *all these files must match the names used in the run prior to
> checkpointing*
> *since we will append to them by default. If you used -deffnm and the
> files*
> *listed above as not present are in fact present, try explicitly
> specifying*
> *them in respective mdrun options. If the files are not available, you can
> add*
> *the -noappend flag to mdrun and write separate new parts. For mere*
> *concatenation of files, you should use the gmx trjcat tool instead.*
>
>
> I do not understand. the input files are correct.
>
> Em qui, 8 de nov de 2018 às 14:13, <
> gromacs.org_gmx-users-request at maillist.sys.kth.se> escreveu:
>
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> >
> > Today's Topics:
> >
> > 1. start the simulation of the last stopping point. (Edjan Silva)
> > 2. Re: start the simulation of the last stopping point. (Paul Bauer)
> > 3. Re: DispErsion correction (Farial Tavakoli)
> > 4. Assigning charge to closely related functional group
> > (Tushar Ranjan Moharana)
> > 5. 4. Re: 5. Re: 3. Re: Strange pullx coordinates (PMF
> > (CROUZY Serge 119222)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Thu, 8 Nov 2018 10:23:13 -0300
> > From: Edjan Silva <edjan.silva at esenfar.ufal.br>
> > To: gromacs.org_gmx-users at maillist.sys.kth.se
> > Subject: [gmx-users] start the simulation of the last stopping point.
> > Message-ID:
> > <
> > CAPf4pyb-pQ8bbTFr3o5SFaSL42JgWvu5kUSLE8L4L8sdi1y-Vg at mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Dear fellow scientists,
> >
> > I'm doing a 40ns simulation between DNA and a small molecule. It occurred
> > that around 30 nanoseconds, the computer hung up.
> >
> > How do I start the simulation from the 30 nanoseconds performed?
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Thu, 8 Nov 2018 14:22:56 +0100
> > From: Paul Bauer <paul.bauer.q at gmail.com>
> > To: gromacs.org_gmx-users at maillist.sys.kth.se
> > Subject: Re: [gmx-users] start the simulation of the last stopping
> > point.
> > Message-ID: <6edfea12-973e-15e2-4d3d-86f67c1dc3d0 at gmail.com>
> > Content-Type: text/plain; charset=utf-8; format=flowed
> >
> > Hello,
> >
> > you can find information on how to extend simulations here:
> >
> >
> http://manual.gromacs.org/documentation/current/user-guide/managing-simulations.html
> >
> > Cheers
> >
> > Paul
> >
> > On 2018-11-08 14:23, Edjan Silva wrote:
> > > Dear fellow scientists,
> > >
> > > I'm doing a 40ns simulation between DNA and a small molecule. It
> occurred
> > > that around 30 nanoseconds, the computer hung up.
> > >
> > > How do I start the simulation from the 30 nanoseconds performed?
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Thu, 8 Nov 2018 19:28:01 +0330
> > From: Farial Tavakoli <faryal.tavakoli at gmail.com>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] DispErsion correction
> > Message-ID:
> > <
> > CADMAFqHWFx8dPb2e8b1xYB6yYVBa93p0Jh3eyfQ6WN5sXcmtgw at mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Dear Justin and Dallas
> >
> > Thank you for your replying
> >
> > I have another problem in minimizing and NVT run of my complex,
> including a
> > protein and a peptidic ligand which the ligand has 2 phosphotyrosine
> > residues. I generated a topology file of ligand using ff14sb in
> ambertools
> > 16 and then converted the .inpcrd and .prmtop files in .gro and .top
> files
> > using acpype python script. The protein topology was generated using
> > amber99sb ff in GROMACS.
> > Then, I cited to gromacs manuscript in order to generate an .itp file of
> > ligand from .top file and generated .itp file by removing the header and
> > footer of .top file in such a way that .itp file starts with :
> > [ moleculetype ]
> > ;name nrexcl
> > mig 3
> >
> > [ atoms ]
> > ; nr type resi res atom cgnr charge mass ; qtot
> > bond_type
> > 1 N3 1 THR N 1 0.181200 14.01000 ; qtot 0.181
> > 2 H 1 THR H1 2 0.193400 1.00800 ; qtot 0.375
> > .
> > .
> > .
> > and ends with
> > 120 123 122 132 1 180.00 4.18400 2 ; C-
> > CD- N- CA
> > 132 135 134 136 1 180.00 43.93200 2 ; CA-
> > O- C- OXT
> > then, modified the complex.gro and .top files according to the tutorials
> in
> > gromacs, I Minimized the complex by issuing this coomand:
> > gmx grompp -f em.mdp -c solv-ions.gro -p topol.top -o em.tpr
> > gmx mdrun -v -defnm em
> > but noticed that the minimization ended soon :
> >
> > Steepest Descents converged to machine precision in 80 steps,
> > but did not reach the requested Fmax < 1000.
> > Potential Energy = -6.5639856e+05
> > Maximum force = 7.0647156e+04 on atom 5256
> > Norm of force = 5.8775842e+02
> >
> > and when performed the NVT run , faced to this error:
> >
> > starting mdrun 'Protein in water'
> > 200000 steps, 400.0 ps.
> > step 0
> > Step 5, time 0.01 (ps) LINCS WARNING
> > relative constraint deviation after LINCS:
> > rms 0.016999, max 0.734404 (between atoms 5258 and 5261)
> > bonds that rotated more than 30 degrees:
> > atom 1 atom 2 angle previous, current, constraint length
> > 5258 5261 90.0 0.0960 0.1665 0.0960
> > 5283 5286 90.0 0.0960 0.1425 0.0960
> > Wrote pdb files with previous and current coordinates
> > .
> > .
> > .
> > It should be noted that atoms 5258 and 5261 are related to sol molecules.
> > TIP3P water model was selected for amber99sb force field.
> > Would you please advice and guild me how should I resolve this problem?
> >
> > Thanks in advance
> > Farial
> >
> >
> > these are the .mdp files that I used:
> > em.mdp file:
> > ; minim.mdp - used as input into grompp to generate em.tpr
> > ; Parameters describing what to do, when to stop and what to save
> > integrator = steep ; Algorithm (steep = steepest descent
> > minimization)
> > emtol = 1000.0 ; Stop minimization when the maximum force <
> > 1000.0 kJ/mol/nm
> > emstep = 0.01 ; Minimization step size
> > nsteps = 50000 ; Maximum number of (minimization) steps to
> > perform
> >
> > ; Parameters describing how to find the neighbors of each atom and how to
> > calculate the interactions
> > nstlist = 1 ; Frequency to update the neighbor list and
> > long range forces
> > cutoff-scheme = Verlet ; Buffered neighbor searching
> > ns_type = grid ; Method to determine neighbor list (simple,
> > grid)
> > coulombtype = PME ; Treatment of long range electrostatic
> > interactions
> > rcoulomb = 1.0 ; Short-range electrostatic cut-off
> > rvdw = 1.0 ; Short-range Van der Waals cut-off
> > pbc = xyz ; Periodic Boundary Conditions in all 3
> > dimensions
> >
> >
> > the nvt.mdp file:
> > title = AMBER NVT equilibration
> > define = -DPOSRES ; position restrain the protein
> > ; Run parameters
> > integrator = md ; leap-frog integrator
> > nsteps = 200000 ; 2 * 200000 = 400 ps
> > dt = 0.002 ; 2 fs
> > ; Output control
> > nstxout = 500 ; save coordinates every 1.0 ps
> > nstvout = 500 ; save velocities every 1.0 ps
> > nstenergy = 500 ; save energies every 1.0 ps
> > nstlog = 500 ; update log file every 1.0 ps
> > ; Bond parameters
> > continuation = no ; first dynamics run
> > constraint_algorithm = lincs ; holonomic constraints
> > constraints = h-bonds ; bonds involving H are constrained
> > lincs_iter = 1 ; accuracy of LINCS
> > lincs_order = 4 ; also related to accuracy
> > ; Nonbonded settings
> > cutoff-scheme = Verlet ; Buffered neighbor searching
> > ns_type = grid ; search neighboring grid cells
> > nstlist = 10 ; 20 fs, largely irrelevant with
> Verlet
> > rcoulomb = 1.0 ; short-range electrostatic cutoff
> (in
> > nm)
> > rvdw = 1.0 ; short-range van der Waals cutoff
> (in
> > nm)
> > ; 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 = V-rescale ; modified Berendsen
> > thermostat
> > tc-grps = Protein Non-Protein ; 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
> > ; Velocity generation
> > gen_vel = yes ; assign velocities from Maxwell
> > distribution
> > gen_temp = 300 ; temperature for Maxwell
> distribution
> > gen_seed = -1 ; generate a random seed
> >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Thu, 8 Nov 2018 21:43:29 +0530
> > From: Tushar Ranjan Moharana <tusharranjanmoharana at gmail.com>
> > To: gromacs.org_gmx-users at maillist.sys.kth.se
> > Subject: [gmx-users] Assigning charge to closely related functional
> > group
> > Message-ID:
> > <
> > CAH6CjFg9p35hiX7HfeYODejws6fs7Z1Bzgmr+zjVOtbDOGL1hw at mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Hi All,
> > Following is the structure of the molecule, which I wish to parameterize.
> > CH3 O
> > | ||
> > CH3 - C - O - C -
> > |
> > CH3
> > It is a peptide capping reagent. The last carbon will form bond with the
> > NH2 group of the peptide. I have generated the the topology using PRODRG
> > server and wish to refine the charge group and partial charges as PRODRG
> > server doen't predict them correctly. The closest well-validated
> structure
> > is of carboxyl ester in the first position of DPPC (or any other
> > glyceride). However there is a minor difference. The carbon attached to
> > three methyl group, in this case is CH0 type and in DPPC it was CH2 type.
> > Since the carbon was part of charge group in DPPC, I fear I may have to
> > change the partial charges. I couldn't find any example where exactly
> same
> > charge group was used. I will appreciate if anyone can suggest me how to
> > assign correct partial charges.
> >
> > Thanks a lot for the help.
> >
> >
> > "A society with free knowledge is better than a society with free food"
> >
> > Tushar Ranjan Moharana
> > B. Tech, NIT Warangal
> > Ph D Student, CCMB
> >
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Thu, 8 Nov 2018 17:12:14 +0000
> > From: CROUZY Serge 119222 <serge.crouzy at cea.fr>
> > To: "gromacs.org_gmx-users at maillist.sys.kth.se"
> > <gromacs.org_gmx-users at maillist.sys.kth.se>
> > Subject: [gmx-users] 4. Re: 5. Re: 3. Re: Strange pullx coordinates
> > (PMF
> > Message-ID:
> > <47AD30A9288C1E49BCF6C0CBB2E5BBA6524B49E4 at EXDAG0-B1.intra.cea.fr
> >
> > Content-Type: text/plain; charset="us-ascii"
> >
> > Hello Justin
> >
> > I still don't understand where Gromacs takes the x coordinates in the
> > output pmf with g_wham
> > If I run g_wham with tpr-files and pullf-files without the pullx-files
> >
> > -it tpr-files.dat -if pullf-files.dat
> > I get a profile which means that g_wham does not take the X-coordinates
> in
> > the pullx (I don't give them), but in the tpr files ...
> > So what X-coordinates are stored in the tpr-files ?
> >
> > Then if I use
> > -it tpr-files.dat -ix pullx-files.dat
> > Where does g_wham take the forces and which x coordinates does it take :
> > those from the tpr or those from the pullx ?
> >
> > Moreover when I restart my simulations, I regenerate new tpr files
> > For instance to add 10 more ns
> >
> > gmx convert-tpr -s umbrella10ns.tpr -extend 10000 -o umbrella20ns.tpr
> > gmx mdrun -s umbrella20ns.tpr -cpi xxx.cpt ....
> >
> > If I run g_wham after this simulation, which tpr should I use ?
> >
> > Can you please explain the role of these tpr in g_wham calculations?
> >
> > Thanks a lot
> >
> > On 11/5/18 5:07 AM, CROUZY Serge 119222 wrote:
> > > Hello Justin-
> > > In MY pullx first column is Time and second column is absolute
> > > coordinate of the COM of the pulled group Maybe we are missing an
> option
> > which would print X and dX in the pullx files - one of the pull-print
> > stuffs ???!!.. In that case too bad we would have tons of "bad" pull
> files
> > Printing the reaction coordinate (dX) should be the default .. Don't you
> > think so ?
> > > Hence my problem with wham using absolute coordinate instead of actual
> > > distance between the two centers of mass What do you suggest to
> retrieve
> > the actual values of my reaction coordinate without rerrunning
> everything ?
> >
> > It should be straightforward to apply a systematic shift to the values in
> > the output PMF curve. But I don't know how you've set up your pull code
> to
> > get such output in the first place. The absolute position of
> > group0 should be totally irrelevant.
> >
> > -Justin
> >
> > > Serge
> > >
> > >
> > *************************
> >
> >
> > ------------------------------
> >
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> >
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