Re: [gmx-users] Difference between equilibration and production run
During the equilibration step the heavy atoms are restrained..So.. You'll not find any movement of these atoms... That's why you can not see that On Tue 25 Jun, 2019, 8:21 AM Neena Susan Eappen, < neena.susaneap...@mail.utoronto.ca> wrote: > Hello gromacs users, > > I used NVT ensemble at constant temperature during > both equilibration and data collection step. I observed that my peptide > turned from extended coil to helical form only in the data collection step > (very early on in the trajectory). Yes, a helical structure is > theoretically expected for my peptide. > > However, I do not understand why I did not see this during equilibration. > The observation is similar regardless of equilibration time. > > Any insight would be appreciated, > Thank you, > Neena > -- > 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] Difference between equilibration and production run
Hello gromacs users, I used NVT ensemble at constant temperature during both equilibration and data collection step. I observed that my peptide turned from extended coil to helical form only in the data collection step (very early on in the trajectory). Yes, a helical structure is theoretically expected for my peptide. However, I do not understand why I did not see this during equilibration. The observation is similar regardless of equilibration time. Any insight would be appreciated, Thank you, Neena -- 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] Error using gmx gangle
Hi everyone: I am trying to use the command of gmx gangle.I have run the following command: gmx gangle -f mapped.xtc -n bonded.ndx -g1 angle -group1 -oav -oall -oh See attachment for input file. However, Segmentation fault (core dumped): Available static index groups: Group 0 "angles" (9 atoms) Specify any number of selections for option 'group1' (First analysis/vector selection): (one per line, for status/groups, 'help' for help, Ctrl-D to end) > 0 Selection '0' parsed Reading frame 0 time 0.000 Segmentation fault (core dumped) Please advise me on how to solve this error. Thank you! -- 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] SMD Pull Direction
Thank you kevin. Will try it shortly. Reza On Tuesday, June 25, 2019, Kevin Boyd wrote: > Hi, > > You can accomplish that using pull-coord1-geometry=direction and an > appropriate vector (0 1 0 for the positive y axis, etc). > > Kevin > > On Mon, Jun 24, 2019 at 3:15 PM Reza Esmaeeli > wrote: > > > Dear Gromacs Users, > > Is there any way to specify the direction of the pull along a certain > axis > > in SMD (i.e. to pull towards a positive or negative end of the Y axis)? > > Thanks, > > Reza > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > https://nam01.safelinks.protection.outlook.com/?url= > http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists% > 2FGMX-Users_Listdata=02%7C01%7Ckevin.boyd%40uconn.edu% > 7Cd8c29c63f6e448cfc25608d6f8d84315%7C17f1a87e2a254eaab9df9d439034 > b080%7C0%7C1%7C636970005072594801sdata=hooPuvbu4er25yBGUJmnsTk5cPKBei > lV14GEsMAXC3s%3Dreserved=0 > > before posting! > > > > * Can't post? Read > > https://nam01.safelinks.protection.outlook.com/?url= > http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists > data=02%7C01%7Ckevin.boyd%40uconn.edu%7Cd8c29c63f6e448cfc25608d6f8d84315% > 7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636970005072604799sdata= > Ni6fkHw9eDLPBpv6Zq3rGoJqgsv4oro4DTi3k3JWebI%3Dreserved=0 > > > > * For (un)subscribe requests visit > > > > https://nam01.safelinks.protection.outlook.com/?url= > https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo% > 2Fgromacs.org_gmx-usersdata=02%7C01%7Ckevin.boyd%40uconn.edu% > 7Cd8c29c63f6e448cfc25608d6f8d84315%7C17f1a87e2a254eaab9df9d439034 > b080%7C0%7C1%7C636970005072604799sdata=aV5NEsKtDI6mj8Ib3hy9l8ex% > 2FUC36s0kCAfwMBKvvJo%3Dreserved=0 > > 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] SMD Pull Direction
Hi, You can accomplish that using pull-coord1-geometry=direction and an appropriate vector (0 1 0 for the positive y axis, etc). Kevin On Mon, Jun 24, 2019 at 3:15 PM Reza Esmaeeli wrote: > Dear Gromacs Users, > Is there any way to specify the direction of the pull along a certain axis > in SMD (i.e. to pull towards a positive or negative end of the Y axis)? > Thanks, > Reza > -- > Gromacs Users mailing list > > * Please search the archive at > https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_Listdata=02%7C01%7Ckevin.boyd%40uconn.edu%7Cd8c29c63f6e448cfc25608d6f8d84315%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636970005072594801sdata=hooPuvbu4er25yBGUJmnsTk5cPKBeilV14GEsMAXC3s%3Dreserved=0 > before posting! > > * Can't post? Read > https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Listsdata=02%7C01%7Ckevin.boyd%40uconn.edu%7Cd8c29c63f6e448cfc25608d6f8d84315%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636970005072604799sdata=Ni6fkHw9eDLPBpv6Zq3rGoJqgsv4oro4DTi3k3JWebI%3Dreserved=0 > > * For (un)subscribe requests visit > > https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-usersdata=02%7C01%7Ckevin.boyd%40uconn.edu%7Cd8c29c63f6e448cfc25608d6f8d84315%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636970005072604799sdata=aV5NEsKtDI6mj8Ib3hy9l8ex%2FUC36s0kCAfwMBKvvJo%3Dreserved=0 > 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] Minimization stops without reaching the requested precision Fmax < 1000
http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Tue, 25 Jun 2019 at 04:03, Mahdi Bagherpoor wrote: > > Dear Gromacs Users, > > I am trying to add the tethrahedral zinc atom dummy model into CHARMM36 > force field in Gromacs. In my system, this dummy zinc interact with four > Cystein residues (CYM). The parameters of the zinc are available in CHARMM > format, which I used to use it in NAMD package. After adding appropriate > parameters, when I do energy minimization, I get this error: > > > Energy minimization has stopped, but the forces have not converged to the > requested precision Fmax < 1000 (which may not be possible for your system). > ... > Steepest Descents converged to machine precision in 1045 steps, > but did not reach the requested Fmax < 1000. > Potential Energy = -1.5922652e+06 > Maximum force = 3.2106902e+07 on atom 3526 > Norm of force = 1.4857810e+05 > > > Atom 3526 is dummy atom of zinc ion. The dummy parameters added in > ffbonded.itp file are: > -- ffbonded.itp > > ;zinc dummy model, bonds > HK ZD 1 0.0900451872.00 > HK HK 1 0.1470451872.00 > ;zinc dummy model, angles > HK ZD HK 5 109.50 460.24 0. > 0.00 > HK HK HK 560.00 460.24 0. > 0.00 > HK HK ZD 535.25 460.24 0. > 0.00 > ;zinc dummy model, dihedrals > ZD HK HK HK 935.30 0.00 2 > HK ZD HK HK 9 120.00 0.00 2 > HK HK HK HK 970.00 0.00 2 > > --- ffnonbonded.itp > > ;zinc dummy model >ZD3061.380.000 A 0.3100 0.1 >HK 1 1.0080000.500 A 0. 0.0 > > = > In contrast to Gromacs, when I do minimization in NAMD, there is no such an > error in minimization. I should mention that I am using single precision > platform of Gromacs. > I would appreciate if you could share me in case you have some ideas about > this problem. > > Cheers, > Mahdi > -- > 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] Kindly help
As noted in previous email and the warning message states, since you are simply trying to add the counter ions and not run a simulation get grompp to ignore the message and continue on i.e. add -maxwarn 1 to the command. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Tue, 25 Jun 2019 at 00:19, kalpana wrote: > > Dear all, > I have worked with the same commands and setting in previous version of > ubuntu and gromacs. Now with new system and up-gradation, I am facing > problem. First kindly see the gmx information and then see the fatal error, > I am getting at grompp. Kindly find the attached ions.mdp as well and see > the other .mdp files too and guide me. > Thanks & Regards > Kalpana > > > 1. > gmx --version > > GROMACS version:2019.3 > Precision: single > Memory model: 64 bit > MPI library:thread_mpi > OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) > GPU support:CUDA > SIMD instructions: AVX_512 > FFT library:fftw-3.3.8-sse2-avx > RDTSCP usage: enabled > TNG support:enabled > Hwloc support: hwloc-1.11.6 > Tracing support:disabled > C compiler: /usr/bin/gcc GNU 8.3.0 > C compiler flags:-mavx512f -mfma -g -fno-inline > C++ compiler: /usr/bin/c++ GNU 8.3.0 > C++ compiler flags: -mavx512f -mfma-std=c++11 -g -fno-inline > CUDA compiler: /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler > driver;Copyright (c) 2005-2019 NVIDIA Corporation;Built on > Wed_Apr_24_19:10:27_PDT_2019;Cuda compilation tools, release 10.1, V10.1.168 > CUDA compiler > flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_75,code=compute_75;-use_fast_math;-D_FORCE_INLINES;; > ;-mavx512f;-mfma;-std=c++11;-g;-fno-inline; > CUDA driver:10.10 > CUDA runtime: N/A > > > 2. > gmx pdb2gmx -f 1model1A1.pdb -o model1_processed.gro -water tip3p > no warning and notes in pdb2gmx run > > 3. > gmx editconf -f model1_processed.gro -o model1_newbox.gro -c -d 1.0 -bt > dodecahedron > no warning and notes in editconf > > 4. > gmx solvate -cp model1_newbox.gro -cs spc216.gro -o model1_solv.gro -p > topol.top > > WARNING: Masses and atomic (Van der Waals) radii will be guessed > based on residue and atom names, since they could not be > definitively assigned from the information in your input > files. These guessed numbers might deviate from the mass > and radius of the atom type. Please check the output > files if necessary. > > NOTE: From version 5.0 gmx solvate uses the Van der Waals radii > from the source below. This means the results may be different > compared to previous GROMACS versions. > > PLEASE READ AND CITE THE FOLLOWING REFERENCE > A. Bondi > van der Waals Volumes and Radii > J. Phys. Chem. 68 (1964) pp. 441-451 > --- Thank You --- > > 5. > gmx grompp -f ions.mdp -c model1_solv.gro -p topol.top -o ions.tpr > > NOTE 1 [file topol.top, line 60959]: > System has non-zero total charge: -13.00 > Total charge should normally be an integer. See > http://www.gromacs.org/Documentation/Floating_Point_Arithmetic > for discussion on how close it should be to an integer. > > WARNING 1 [file topol.top, line 60959]: > You are using Ewald electrostatics in a system with net charge. This can > lead to severe artifacts, such as ions moving into regions with low > dielectric, due to the uniform background charge. We suggest to > neutralize your system with counter ions, possibly in combination with a > physiological salt concentration. > > PLEASE READ AND CITE THE FOLLOWING REFERENCE > J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof > Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a > Net > Charge > J. Chem. Theory Comput. 10 (2014) pp. 381-393 > --- Thank You --- > > Removing all charge groups because cutoff-scheme=Verlet > Analysing residue names: > There are: 424Protein residues > There are: 16060 Water residues > Analysing Protein... > Number of degrees of freedom in T-Coupling group rest is 115683.00 > Calculating fourier grid dimensions for X Y Z > Using a fourier grid of 80x80x80, spacing 0.116 0.116 0.116 > Estimate for the relative computational load of the PME mesh part: 0.34 > This run will generate roughly 4 Mb of data > > There was 1 note > > There was 1 warning > >
Re: [gmx-users] Check point file
Note the .cpt file is a snap shot file, like a .gro coordinate file. It saves the state of the system at a particular point of time in a manner that you can have an exact restart at that time. You can still continue from 80ns relatively closely using the appropriate files you already have, you are not starting a "brand new" simulation. You can also join together the trajectory and energy files once it is completed. gmx grompp -f 400Kfor20ns.mdp -p topol.top -c 80ns.gro -e 0-80ns.edr -o continuation.tpr gmx mdrun -s continuation.tpr Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Tue, 25 Jun 2019 at 01:08, Alex wrote: > > Hi Mark > Actually the simulation I am talking about is an annealing simulation in > which the system are being annealed from room temperature to 400 k during a > 80 ns simulation and then the temperature are being ramped down again to be > at room temperature at 100 ns. Now I just want to keep continuing the > annealing from 80 ns (keeping the temperature at 400 k) instead of ramping > down. And If I start a completely brand new simulation the way you > mentioned, it does not continue the simulation at the annealed temperature > of my previous simulation. > I wish the state.cpt was also truncate-able likes the xtc and trr files to > have all at 80 ns. > > Regards, > Alex > > On Mon, Jun 24, 2019 at 5:41 AM Mark Abraham > wrote: > > > Hi, > > > > On Mon., 24 Jun. 2019, 11:21 Alex, wrote: > > > > > Thanks Mark. > > > With not be able to append to the simulation files, you mean, I should > > not > > > use the "-cpi state.cpt" in the gmx mdrun, right? > > > > > > No, I mean you can't use -append. You have no relevant file for -cpi. > > > > > If > > > > > so, then, the > > > simulation is a completely brand new simulation excepts that it use -c > > > case.80ns.gro file as starting frame from t = 0.0. Then does the > > > trjcat/eneconv used for later concatenation know that the new outputs > > > should be assigned to the time t = 8000*1*? > > > > > > > The link I gave earlier has hints for how to prepare for this to go > > smoothly. > > > > In the other case, if I use the -cpi state.cpt in the gmx mdrun, everything > > > are being continued from t = 10. > > > > > > > Yes > > > > Mark > > > > > > > Thank you. > > > Alex > > > > > > On Mon, Jun 24, 2019 at 1:55 AM Mark Abraham > > > wrote: > > > > > > > Hi, > > > > > > > > No, that isn't meaningful. Follow > > > > > > > > > > > > > http://manual.gromacs.org/current/user-guide/managing-simulations.html#changing-mdp-options-for-a-restart > > > > but > > > > for the -c option, pass a file containing the desired frame extracted > > > from > > > > your .trr file. You will not be able to append to the simulation files, > > > but > > > > once the simulation is complete, you can concatenate all the files with > > > > trjcat/eneconv. > > > > > > > > Mark > > > > > > > > On Sun, 23 Jun 2019 at 22:53, Alex wrote: > > > > > > > > > Dear all, > > > > > I have a 100 ns simulation, the case.100ns.xtc, case.100ns.trr, > > > > > case.100ns.cpt ... all are here, I want to truncate the xtc file at > > 80 > > > > ns > > > > > (case.80ns.xtc, case.80ns.trr) and continue it by using a new tpr > > file. > > > > > Everything is clear for me except the case.cpt file for which is not > > > > > possible to have the case.80ns.cpt unlike the case.80ns.xtc and trr. > > > > > So, I wonder if it is meaningful if I use the case.100ns.cpt,, > > > > > case.80ns.xtc and case.80ns.trr to continue from 80 ns point? > > > > > > > > > > Thank you. > > > > > Alex > > > > > -- > > > > > 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
[gmx-users] SMD Pull Direction
Dear Gromacs Users, Is there any way to specify the direction of the pull along a certain axis in SMD (i.e. to pull towards a positive or negative end of the Y axis)? Thanks, Reza -- 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] problem regarding gmx wham
Dear all, I am trying to use gmx wham to compute a potential of mean force. I set the umbrella sampling options in the .mdp file as: pull= yes pull_ngroups= 1 pull_ncoords= 1 pull-print-components = yes pull-print-com = yes pull-print-ref-value= yes pull_group1_name= chain_P pull-coord1-origin = 0.0 0.0 5.266 pull_coord1_dim = N N Y pull_coord1_type= umbrella pull_coord1_geometry= distance pull_coord1_groups = 0 1 pull_coord1_rate= 0.0 pull_coord1_k = 2092 pull_coord1_start = yes I have used the command line: gmx wham -it tpr-files.dat -ix pullx-files.dat -o -hist -unit kCal *Fatal error:* *gmx wham cannot read pullx files if the components of the coordinate was written.*I really cannot think of why is it giving me that? Any kind of advice/suggestions will be deeply appreciated. Thanks in advance, San -- 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] Minimization stops without reaching the requested precision Fmax < 1000
Dear Gromacs Users, I am trying to add the tethrahedral zinc atom dummy model into CHARMM36 force field in Gromacs. In my system, this dummy zinc interact with four Cystein residues (CYM). The parameters of the zinc are available in CHARMM format, which I used to use it in NAMD package. After adding appropriate parameters, when I do energy minimization, I get this error: Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1000 (which may not be possible for your system). ... Steepest Descents converged to machine precision in 1045 steps, but did not reach the requested Fmax < 1000. Potential Energy = -1.5922652e+06 Maximum force = 3.2106902e+07 on atom 3526 Norm of force = 1.4857810e+05 Atom 3526 is dummy atom of zinc ion. The dummy parameters added in ffbonded.itp file are: -- ffbonded.itp ;zinc dummy model, bonds HK ZD 1 0.0900451872.00 HK HK 1 0.1470451872.00 ;zinc dummy model, angles HK ZD HK 5 109.50 460.24 0. 0.00 HK HK HK 560.00 460.24 0. 0.00 HK HK ZD 535.25 460.24 0. 0.00 ;zinc dummy model, dihedrals ZD HK HK HK 935.30 0.00 2 HK ZD HK HK 9 120.00 0.00 2 HK HK HK HK 970.00 0.00 2 --- ffnonbonded.itp ;zinc dummy model ZD3061.380.000 A 0.3100 0.1 HK 1 1.0080000.500 A 0. 0.0 = In contrast to Gromacs, when I do minimization in NAMD, there is no such an error in minimization. I should mention that I am using single precision platform of Gromacs. I would appreciate if you could share me in case you have some ideas about this problem. Cheers, Mahdi -- 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] Check point file
Hi Mark Actually the simulation I am talking about is an annealing simulation in which the system are being annealed from room temperature to 400 k during a 80 ns simulation and then the temperature are being ramped down again to be at room temperature at 100 ns. Now I just want to keep continuing the annealing from 80 ns (keeping the temperature at 400 k) instead of ramping down. And If I start a completely brand new simulation the way you mentioned, it does not continue the simulation at the annealed temperature of my previous simulation. I wish the state.cpt was also truncate-able likes the xtc and trr files to have all at 80 ns. Regards, Alex On Mon, Jun 24, 2019 at 5:41 AM Mark Abraham wrote: > Hi, > > On Mon., 24 Jun. 2019, 11:21 Alex, wrote: > > > Thanks Mark. > > With not be able to append to the simulation files, you mean, I should > not > > use the "-cpi state.cpt" in the gmx mdrun, right? > > > No, I mean you can't use -append. You have no relevant file for -cpi. > > > If > > > so, then, the > > simulation is a completely brand new simulation excepts that it use -c > > case.80ns.gro file as starting frame from t = 0.0. Then does the > > trjcat/eneconv used for later concatenation know that the new outputs > > should be assigned to the time t = 8000*1*? > > > > The link I gave earlier has hints for how to prepare for this to go > smoothly. > > In the other case, if I use the -cpi state.cpt in the gmx mdrun, everything > > are being continued from t = 10. > > > > Yes > > Mark > > > > Thank you. > > Alex > > > > On Mon, Jun 24, 2019 at 1:55 AM Mark Abraham > > wrote: > > > > > Hi, > > > > > > No, that isn't meaningful. Follow > > > > > > > > > http://manual.gromacs.org/current/user-guide/managing-simulations.html#changing-mdp-options-for-a-restart > > > but > > > for the -c option, pass a file containing the desired frame extracted > > from > > > your .trr file. You will not be able to append to the simulation files, > > but > > > once the simulation is complete, you can concatenate all the files with > > > trjcat/eneconv. > > > > > > Mark > > > > > > On Sun, 23 Jun 2019 at 22:53, Alex wrote: > > > > > > > Dear all, > > > > I have a 100 ns simulation, the case.100ns.xtc, case.100ns.trr, > > > > case.100ns.cpt ... all are here, I want to truncate the xtc file at > 80 > > > ns > > > > (case.80ns.xtc, case.80ns.trr) and continue it by using a new tpr > file. > > > > Everything is clear for me except the case.cpt file for which is not > > > > possible to have the case.80ns.cpt unlike the case.80ns.xtc and trr. > > > > So, I wonder if it is meaningful if I use the case.100ns.cpt,, > > > > case.80ns.xtc and case.80ns.trr to continue from 80 ns point? > > > > > > > > Thank you. > > > > Alex > > > > -- > > > > 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.
[gmx-users] Kindly help
Dear all, I have worked with the same commands and setting in previous version of ubuntu and gromacs. Now with new system and up-gradation, I am facing problem. First kindly see the gmx information and then see the fatal error, I am getting at grompp. Kindly find the attached ions.mdp as well and see the other .mdp files too and guide me. Thanks & Regards Kalpana 1. gmx --version GROMACS version:2019.3 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support:CUDA SIMD instructions: AVX_512 FFT library:fftw-3.3.8-sse2-avx RDTSCP usage: enabled TNG support:enabled Hwloc support: hwloc-1.11.6 Tracing support:disabled C compiler: /usr/bin/gcc GNU 8.3.0 C compiler flags:-mavx512f -mfma -g -fno-inline C++ compiler: /usr/bin/c++ GNU 8.3.0 C++ compiler flags: -mavx512f -mfma-std=c++11 -g -fno-inline CUDA compiler: /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2019 NVIDIA Corporation;Built on Wed_Apr_24_19:10:27_PDT_2019;Cuda compilation tools, release 10.1, V10.1.168 CUDA compiler flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_75,code=compute_75;-use_fast_math;-D_FORCE_INLINES;; ;-mavx512f;-mfma;-std=c++11;-g;-fno-inline; CUDA driver:10.10 CUDA runtime: N/A 2. gmx pdb2gmx -f 1model1A1.pdb -o model1_processed.gro -water tip3p no warning and notes in pdb2gmx run 3. gmx editconf -f model1_processed.gro -o model1_newbox.gro -c -d 1.0 -bt dodecahedron no warning and notes in editconf 4. gmx solvate -cp model1_newbox.gro -cs spc216.gro -o model1_solv.gro -p topol.top WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. NOTE: From version 5.0 gmx solvate uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. PLEASE READ AND CITE THE FOLLOWING REFERENCE A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 --- Thank You --- 5. gmx grompp -f ions.mdp -c model1_solv.gro -p topol.top -o ions.tpr NOTE 1 [file topol.top, line 60959]: System has non-zero total charge: -13.00 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. WARNING 1 [file topol.top, line 60959]: You are using Ewald electrostatics in a system with net charge. This can lead to severe artifacts, such as ions moving into regions with low dielectric, due to the uniform background charge. We suggest to neutralize your system with counter ions, possibly in combination with a physiological salt concentration. PLEASE READ AND CITE THE FOLLOWING REFERENCE J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge J. Chem. Theory Comput. 10 (2014) pp. 381-393 --- Thank You --- Removing all charge groups because cutoff-scheme=Verlet Analysing residue names: There are: 424Protein residues There are: 16060 Water residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 115683.00 Calculating fourier grid dimensions for X Y Z Using a fourier grid of 80x80x80, spacing 0.116 0.116 0.116 Estimate for the relative computational load of the PME mesh part: 0.34 This run will generate roughly 4 Mb of data There was 1 note There was 1 warning --- Program: gmx grompp, version 2019.3 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2315) Fatal error: Too many warnings (1). If you are sure all warnings are harmless, use the -maxwarn option. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- -- 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] GROMOS FF conversion
I've not used this myself, but you can get them from: http://vienna-ptm.univie.ac.at/?page_id=100 IIRC there are also conversion scripts on the GROMACS website too (in the user contributions). Cheers Tom On 24/06/2019 13:55, András Ferenc WACHA wrote: Dear List, I would like to use the 54a8 version of the GROMOS FF with GROMACS. I have seen that version 54a7 is already supplied "out of the box". Before starting to develop a conversion script, I would like to ask if anyone has information on how the previous versions were converted, and if there already exists a validated mechanism. Googling on the topic did not help me much. Kind regards, Andras -- Dr Thomas Piggot Visiting Fellow University of Southampton, UK. -- 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] GROMOS FF conversion
Dear List, I would like to use the 54a8 version of the GROMOS FF with GROMACS. I have seen that version 54a7 is already supplied "out of the box". Before starting to develop a conversion script, I would like to ask if anyone has information on how the previous versions were converted, and if there already exists a validated mechanism. Googling on the topic did not help me much. Kind regards, Andras -- András Ferenc Wacha, PhD research fellow, CREDO instrument responsible Biological Nanochemistry Research Group Institute of Materials and Environmental Chemistry Research Centre for Natural Sciences Hungarian Academy of Sciences (RCNS HAS) Magyar tudósok körútja 2. H-1117 Budapest, Hungary Phone: +36-1-382-6427 Web: http://bionano.ttk.mta.hu, CREDO SAXS instrument: http://credo.ttk.mta.hu signature.asc Description: OpenPGP digital signature -- 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] Fwd: (-13.000000 Total charge should normally be an integer), Facing problem while running gromacs
This shows why posting the entire output is important. The note is not the reason why grompp failed, the warning is what you need to take note of and respond to/deal with. If you are doing the step here to add the counter-ions to neutralise charge, then do as the information at the bottom is telling you to do, ignore the warning and proceed. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Mon, 24 Jun 2019 at 18:54, kalpana wrote: > > Thanks a lot for your prompt response. I thought the fetal error is due to > as its saying non-interger charge but i am not getting the output file to > add ions to neutralize charge. The complete report is this: > > gmx grompp -f ions.mdp -c model1_solv.gro -p topol.top -o ions.tpr > > Setting the LD random seed to -1944004748 > Generated 330891 of the 330891 non-bonded parameter combinations > Generating 1-4 interactions: fudge = 0.5 > Generated 330891 of the 330891 1-4 parameter combinations > Excluding 3 bonded neighbours molecule type 'Protein_chain_A' > Excluding 2 bonded neighbours molecule type 'SOL' > > NOTE 1 [file topol.top, line 60959]: > System has non-zero total charge: -13.00 > Total charge should normally be an integer. See > http://www.gromacs.org/Documentation/Floating_Point_Arithmetic > for discussion on how close it should be to an integer. > > > > > WARNING 1 [file topol.top, line 60959]: > You are using Ewald electrostatics in a system with net charge. This can > lead to severe artifacts, such as ions moving into regions with low > dielectric, due to the uniform background charge. We suggest to > neutralize your system with counter ions, possibly in combination with a > physiological salt concentration. > > > PLEASE READ AND CITE THE FOLLOWING REFERENCE > J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof > Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a > Net > Charge > J. Chem. Theory Comput. 10 (2014) pp. 381-393 > --- Thank You --- > > Cleaning up constraints and constant bonded interactions with virtual sites > Removing all charge groups because cutoff-scheme=Verlet > Analysing residue names: > There are: 424Protein residues > There are: 16324 Water residues > Analysing Protein... > Number of degrees of freedom in T-Coupling group rest is 117267.00 > Calculating fourier grid dimensions for X Y Z > Using a fourier grid of 80x80x80, spacing 0.116 0.116 0.116 > Estimate for the relative computational load of the PME mesh part: 0.26 > This run will generate roughly 6 Mb of data > > There was 1 note > > There was 1 warning > > --- > Program: gmx grompp, version 2019.3 > Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2315) > > Fatal error: > Too many warnings (1). > If you are sure all warnings are harmless, use the -maxwarn option. > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > --- > > On Mon, Jun 24, 2019 at 11:22 AM Bratin Kumar Das < > 177cy500.bra...@nitk.edu.in> wrote: > > > It is telling that system have -13 charge...Which need to be neutralise by > > gmx genion command > > > > On Mon 24 Jun, 2019, 11:09 AM Alex, wrote: > > > > > It is not an error message, but a note. If grompp quits with an error, > > > please read it carefully. > > > > > > Alex > > > > > > On 6/23/2019 11:27 PM, kalpana wrote: > > > > Kindly help to understand this error message becz with previous > > > > installation with same setting files, there was no error. The error > > > message > > > > is as follows: > > > > > > > >gmx grompp -f ions.mdp -c model1_solv.gro -p topol.top > > -o > > > > ions.tpr > > > > > > > >Setting the LD random seed to 31221519 > > > >Generated 330891 of the 330891 non-bonded parameter > > > > combinations > > > >Generating 1-4 interactions: fudge = 0.5 > > > >Generated 330891 of the 330891 1-4 parameter > > combinations > > > >Excluding 3 bonded neighbours molecule type > > > 'Protein_chain_A' > > > >Excluding 2 bonded neighbours molecule type 'SOL' > > > > > > > >NOTE 1 [file topol.top, line 60959]: > > > >System has non-zero total charge: -13.00 > > > >Total charge should normally be an integer. See > > > > > > > http://www.gromacs.org/Documentation/Floating_Point_Arithmetic > > > >for discussion on how close it should be to an integer. > > > > > > > > Best regards > > > > Kalpana > > > -- > >
Re: [gmx-users] Error gmx pdb2gro
Bump.. On Sat, 22 Jun 2019, 00:35 Danilo Boskovic, wrote: > OK. And could you explain how? I just started to learn doing simulations > and am an undergraduate. Can't find any documentation on what you said I > need to do. > > On Fri, 21 Jun 2019, 16:11 Justin Lemkul, wrote: > >> >> >> On 6/21/19 8:14 AM, Danilo Boskovic wrote: >> > I am trying to backmap an RNA file from the MARTINI tutorial as stated >> in >> > the tutorial but i am getting error atom N not found in buiding block >> while >> > combining tdb and rtp when trying to generate a topology file. Im using >> > Gromacs 2018.7. It also says >> > >> > Start terminus U-501: NH3+ >> > End terminus A-511: COO- >> > >> > for an RNA. >> > >> > Example first three lines of PDB file: >> > >> > ATOM 1 C5' U B 501 23.332 8.576 -5.633 1.00 4.88 >> >C >> > ATOM 2 O5' U B 501 24.120 9.582 -6.276 1.00 5.15 >> >O >> > ATOM 3 C4' U B 501 24.186 7.735 -4.679 1.00 4.12 >> >C >> > >> > It seems that the format of the PDB is recognized as a protein. I am >> using >> > CHARMM and tip3p. I have a tip3p.itp file, tried to use #include but it >> did >> > not help. For full tutorial: >> > >> http://cgmartini.nl/index.php/tutorials-general-introduction-gmx5/tutorial-martini-rna-gmx5 >> >> You have to manually choose termini with CHARMM36. This is because there >> is no way to split proteins, nucleic acids, etc. into their own files >> automatically when reading in the whole force field and we try to avoid >> hard-coding as much as we possibly can. >> >> -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 >> >> == >> >> -- >> 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] Check point file
Hi, On Mon., 24 Jun. 2019, 11:21 Alex, wrote: > Thanks Mark. > With not be able to append to the simulation files, you mean, I should not > use the "-cpi state.cpt" in the gmx mdrun, right? No, I mean you can't use -append. You have no relevant file for -cpi. > If > so, then, the > simulation is a completely brand new simulation excepts that it use -c > case.80ns.gro file as starting frame from t = 0.0. Then does the > trjcat/eneconv used for later concatenation know that the new outputs > should be assigned to the time t = 8000*1*? > The link I gave earlier has hints for how to prepare for this to go smoothly. In the other case, if I use the -cpi state.cpt in the gmx mdrun, everything > are being continued from t = 10. > Yes Mark > Thank you. > Alex > > On Mon, Jun 24, 2019 at 1:55 AM Mark Abraham > wrote: > > > Hi, > > > > No, that isn't meaningful. Follow > > > > > http://manual.gromacs.org/current/user-guide/managing-simulations.html#changing-mdp-options-for-a-restart > > but > > for the -c option, pass a file containing the desired frame extracted > from > > your .trr file. You will not be able to append to the simulation files, > but > > once the simulation is complete, you can concatenate all the files with > > trjcat/eneconv. > > > > Mark > > > > On Sun, 23 Jun 2019 at 22:53, Alex wrote: > > > > > Dear all, > > > I have a 100 ns simulation, the case.100ns.xtc, case.100ns.trr, > > > case.100ns.cpt ... all are here, I want to truncate the xtc file at 80 > > ns > > > (case.80ns.xtc, case.80ns.trr) and continue it by using a new tpr file. > > > Everything is clear for me except the case.cpt file for which is not > > > possible to have the case.80ns.cpt unlike the case.80ns.xtc and trr. > > > So, I wonder if it is meaningful if I use the case.100ns.cpt,, > > > case.80ns.xtc and case.80ns.trr to continue from 80 ns point? > > > > > > Thank you. > > > Alex > > > -- > > > 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] Check point file
Thanks Mark. With not be able to append to the simulation files, you mean, I should not use the "-cpi state.cpt" in the gmx mdrun, right? If so, then, the simulation is a completely brand new simulation excepts that it use -c case.80ns.gro file as starting frame from t = 0.0. Then does the trjcat/eneconv used for later concatenation know that the new outputs should be assigned to the time t = 8000*1*? In the other case, if I use the -cpi state.cpt in the gmx mdrun, everything are being continued from t = 10. Thank you. Alex On Mon, Jun 24, 2019 at 1:55 AM Mark Abraham wrote: > Hi, > > No, that isn't meaningful. Follow > > http://manual.gromacs.org/current/user-guide/managing-simulations.html#changing-mdp-options-for-a-restart > but > for the -c option, pass a file containing the desired frame extracted from > your .trr file. You will not be able to append to the simulation files, but > once the simulation is complete, you can concatenate all the files with > trjcat/eneconv. > > Mark > > On Sun, 23 Jun 2019 at 22:53, Alex wrote: > > > Dear all, > > I have a 100 ns simulation, the case.100ns.xtc, case.100ns.trr, > > case.100ns.cpt ... all are here, I want to truncate the xtc file at 80 > ns > > (case.80ns.xtc, case.80ns.trr) and continue it by using a new tpr file. > > Everything is clear for me except the case.cpt file for which is not > > possible to have the case.80ns.cpt unlike the case.80ns.xtc and trr. > > So, I wonder if it is meaningful if I use the case.100ns.cpt,, > > case.80ns.xtc and case.80ns.trr to continue from 80 ns point? > > > > Thank you. > > Alex > > -- > > 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] Fwd: (-13.000000 Total charge should normally be an integer), Facing problem while running gromacs
Thanks a lot for your prompt response. I thought the fetal error is due to as its saying non-interger charge but i am not getting the output file to add ions to neutralize charge. The complete report is this: gmx grompp -f ions.mdp -c model1_solv.gro -p topol.top -o ions.tpr Setting the LD random seed to -1944004748 Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file topol.top, line 60959]: System has non-zero total charge: -13.00 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. WARNING 1 [file topol.top, line 60959]: You are using Ewald electrostatics in a system with net charge. This can lead to severe artifacts, such as ions moving into regions with low dielectric, due to the uniform background charge. We suggest to neutralize your system with counter ions, possibly in combination with a physiological salt concentration. PLEASE READ AND CITE THE FOLLOWING REFERENCE J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge J. Chem. Theory Comput. 10 (2014) pp. 381-393 --- Thank You --- Cleaning up constraints and constant bonded interactions with virtual sites Removing all charge groups because cutoff-scheme=Verlet Analysing residue names: There are: 424Protein residues There are: 16324 Water residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 117267.00 Calculating fourier grid dimensions for X Y Z Using a fourier grid of 80x80x80, spacing 0.116 0.116 0.116 Estimate for the relative computational load of the PME mesh part: 0.26 This run will generate roughly 6 Mb of data There was 1 note There was 1 warning --- Program: gmx grompp, version 2019.3 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2315) Fatal error: Too many warnings (1). If you are sure all warnings are harmless, use the -maxwarn option. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- On Mon, Jun 24, 2019 at 11:22 AM Bratin Kumar Das < 177cy500.bra...@nitk.edu.in> wrote: > It is telling that system have -13 charge...Which need to be neutralise by > gmx genion command > > On Mon 24 Jun, 2019, 11:09 AM Alex, wrote: > > > It is not an error message, but a note. If grompp quits with an error, > > please read it carefully. > > > > Alex > > > > On 6/23/2019 11:27 PM, kalpana wrote: > > > Kindly help to understand this error message becz with previous > > > installation with same setting files, there was no error. The error > > message > > > is as follows: > > > > > >gmx grompp -f ions.mdp -c model1_solv.gro -p topol.top > -o > > > ions.tpr > > > > > >Setting the LD random seed to 31221519 > > >Generated 330891 of the 330891 non-bonded parameter > > > combinations > > >Generating 1-4 interactions: fudge = 0.5 > > >Generated 330891 of the 330891 1-4 parameter > combinations > > >Excluding 3 bonded neighbours molecule type > > 'Protein_chain_A' > > >Excluding 2 bonded neighbours molecule type 'SOL' > > > > > >NOTE 1 [file topol.top, line 60959]: > > >System has non-zero total charge: -13.00 > > >Total charge should normally be an integer. See > > > > > http://www.gromacs.org/Documentation/Floating_Point_Arithmetic > > >for discussion on how close it should be to an integer. > > > > > > Best regards > > > Kalpana > > -- > > 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
Re: [gmx-users] Amber force field for metal Surface
The suggestion is to proceed with reading literature even if acpype succeeds in generating some sort of a topology. In general, interactions with a metal surface cannot be adequately modeled with biomolecular-style forcefields using fixed partial charges + LJ. Depending on what the end goal is, it may or may not be appropriate to use Gromacs for this purpose, but it needs to be a judicious, carefully researched choice. Alex On 6/24/2019 12:50 AM, Kumari Shilpa wrote: I am calculating interaction energy between a polymer molecule (75 atoms) and an iron surface. For polymer I generated an itp file (based on Amber force field) using acpype. But acpype is able to generate the itp File only for polymer, once I incorporate iron in the xyz file, it doesn't work. Could anyone please suggest how to Proceed further? How to include forcefield parameters for FE in the existing itp file for polymer? -- 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] Amber force field for metal Surface
I am calculating interaction energy between a polymer molecule (75 atoms) and an iron surface. For polymer I generated an itp file (based on Amber force field) using acpype. But acpype is able to generate the itp File only for polymer, once I incorporate iron in the xyz file, it doesn't work. Could anyone please suggest how to Proceed further? How to include forcefield parameters for FE in the existing itp file for polymer? -- 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] Fwd: (-13.000000 Total charge should normally be an integer), Facing problem while running gromacs
A good place to always check for a GROMACS error is http://manual.gromacs.org/current/user-guide/run-time-errors.html Particular entry you want is: http://manual.gromacs.org/current/user-guide/run-time-errors.html#system-has-non-zero-total-charge Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Mon, 24 Jun 2019 at 15:30, kalpana wrote: > > Kindly help to understand this error message becz with previous > installation with same setting files, there was no error. The error message > is as follows: > > gmx grompp -f ions.mdp -c model1_solv.gro -p topol.top -o > ions.tpr > > Setting the LD random seed to 31221519 > Generated 330891 of the 330891 non-bonded parameter > combinations > Generating 1-4 interactions: fudge = 0.5 > Generated 330891 of the 330891 1-4 parameter combinations > Excluding 3 bonded neighbours molecule type 'Protein_chain_A' > Excluding 2 bonded neighbours molecule type 'SOL' > > NOTE 1 [file topol.top, line 60959]: > System has non-zero total charge: -13.00 > Total charge should normally be an integer. See > http://www.gromacs.org/Documentation/Floating_Point_Arithmetic > for discussion on how close it should be to an integer. > > Best regards > Kalpana > -- > 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.
