[gmx-users] gromacs.org_gmx-users Digest, Vol 175, Issue 28 - start the simulation of the last stopping point.
Edjan Silva
edjan.silva at esenfar.ufal.br
Fri Nov 9 14:11:26 CET 2018
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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> End of gromacs.org_gmx-users Digest, Vol 175, Issue 28
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