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.si...@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-requ...@maillist.sys.kth.se> escreveu: > > > Send gromacs.org_gmx-users mailing list submissions to > > gromacs.org_gmx-users@maillist.sys.kth.se > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > or, via email, send a message with subject or body 'help' to > > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > > > You can reach the person managing the list at > > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of gromacs.org_gmx-users digest..." > > > > > > 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.si...@esenfar.ufal.br> > > To: gromacs.org_gmx-users@maillist.sys.kth.se > > Subject: [gmx-users] start the simulation of the last stopping point. > > Message-ID: > > < > > capf4pyb-pq8bbtfr3o5sfasl42jgwvu5kusle8l4l8sdi1y...@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.baue...@gmail.com> > > To: gromacs.org_gmx-users@maillist.sys.kth.se > > Subject: Re: [gmx-users] start the simulation of the last stopping > > point. > > Message-ID: <6edfea12-973e-15e2-4d3d-86f67c1dc...@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.tavak...@gmail.com> > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] DispErsion correction > > Message-ID: > > < > > cadmafqhwfx8dpb2e8b1xyb6yyvba93p0jh3eyfq6wn5sxcm...@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 <tusharranjanmohar...@gmail.com> > > To: gromacs.org_gmx-users@maillist.sys.kth.se > > Subject: [gmx-users] Assigning charge to closely related functional > > group > > Message-ID: > > < > > cah6cjfg9p35hix7hfeyodejws6fs7z1bzgmr+zjvotbdogl...@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.cro...@cea.fr> > > To: "gromacs.org_gmx-users@maillist.sys.kth.se" > > <gromacs.org_gmx-users@maillist.sys.kth.se> > > Subject: [gmx-users] 4. Re: 5. Re: 3. Re: Strange pullx coordinates > > (PMF > > Message-ID: > > <47ad30a9288c1e49bcf6c0cbb2e5bba6524b4...@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 > > > > > > > > ************************* > > > > > > ------------------------------ > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? 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