[gmx-users] Help with segmentation fault error
Hi, I have installed 5.1.1, and am trying to run the simulations. During the run, I am getting this error as pasted below: WARNING: Listed nonbonded interaction between particles 1 and 9 at distance 9.500 which is larger than the table limit 2.030 nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. Segmentation fault (core dumped) I have tried neutralizing the the charges, however, the error remains the same. I am using the NVT parameters as below: title= OPLS Lysozyme NVT equilibration define= -DPOSRES; position restrain the protein ; Run parameters integrator= md; leap-frog integrator nsteps= 1; 2 * 5 = 100 ps dt= 0.002; 2 fs ; Output control nstxout= 1000; save coordinates every 1.0 ps nstvout= 1000; save velocities every 1.0 ps nstenergy= 1000; save energies every 1.0 ps nstlog= 1000; update log file every 1.0 ps ; Bond parameters continuation= no; first dynamics run constraint_algorithm= lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet 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 ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= yes; assign velocities from Maxwell distribution gen_temp= 300; temperature for Maxwell distribution gen_seed= -1; generate a random seed When using on an older Gromacs version (older than 5.1), the run is smooth (everything else remaining constant). Can anyone help me to target the error? Whether it is due my hardware issue (its a dell inspiron with 4 GB RAM, i5 processor, 2 cores, 1.7 GHz) or I am making an error in the steps? Thanks, Kunal -- Dr. Kunal Maniar Resident, Department of Pharmacology, Post Graduate Institute of Medical Education and Research, Chandigarh (PGIMER) Mobile: +91 8968630447 Email id: drkunalman...@gmail.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.
Re: [gmx-users] question about gmx do_dssp
Dear Mark, Thank you, I have figure out the problem, but to my surprise, the output xpm file lack the information of the last residue for the CHARMM27 force file (charmm's trajectory is good), but not for other force field. I wonder whether the DSSP program in the gromacs ignore the last residue of structures generated by CHARMM27 force field. Best regards, Ouyang At 2017-08-04 22:32:25, "Mark Abraham" wrote: >Hi, > >Isn't that figure what is in the xpm file? > >Mark > >On Fri, Aug 4, 2017 at 4:20 PM YanhuaOuyang <15901283...@163.com> wrote: > >> Hi, >>I have run a MD simulation and used gmx do_dssp to calculate the >> secondary structure content. The output files are md_dssp.xpm and >> scount.xvg. I want to know that each residue belongs to what kind of >> secondary structure for each frame. But the scount.xvg output file only >> have the number of residues with each secondary structure and the total >> secondary structure count as a function of time. So, can I get the >> information on "each residue belongs to which kind of secondary structure >> for each frame" to draw a figure of " amino acid vs secondary structure" ? >> >> Best regards, >> Ouyang >> -- >> 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] Generating topology file for a long polymer chain
Dear gmx-users, I am trying to build a polymer box from scratch and generate the required input files. So far, I did these steps: 1. built a chain of the polymer 2. run ACPYPE to generate the topology file... However, since the chain is long, it took so long time with ACPYPE and the calculation is timed out without convergence. - Is it possible to restart the ACPYPE calculation? I read in some tutorials that it is also possible to run the ACPYPE calculations for the monomeric unit instead and repeat its parameters for the whole chain. How is it possible? The polymer chain may have a conformation with different angles and dihedrals than in the monomer. In general, how can I use the topology file of a monomer for the longer chain of a polymer ? Could you please advise me? Best regards, Mahsa -- 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] Generating topology file for a long polymer chain
Dear gmx-users, I am trying to build a polymer box from scratch and generate the required input files. So far, I did these steps: 1. built a chain of the polymer 2. run ACPYPE to generate the topology file... However, since the chain is long, it took so long time with ACPYPE and the calculation is timed out without convergence. - Is it possible to restart the ACPYPE calculation? I read in some tutorials that it is also possible to run the ACPYPE calculations for the monomeric unit instead and repeat its parameters for the whole chain. How is it possible? The polymer chain may have a conformation with different angles and dihedrals than in the monomer. In general, how can I use the topology file of a monomer for the longer chain of a polymer? Could you please advise me? Best regards, Mahsa -- 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] QSUB commands
Hi gromacs users, I use cygwin terminal in windows 7, 64 bit computer. How to use qsub commands and thereby do gromacs simulations in a cluster? Can anyone tell me clearly? Thanks, Neha -- 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] Umbrella Sampling -PME
Hello, will decouple intramuscular interactions during windows simulation impact the accuracy of the PME estimated? I am pulling large molecule Regards -- 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] question about gmx do_dssp
Hi, I'd start by checking if that last residue is a normal one... Mark On Sat, Aug 5, 2017 at 2:02 PM YanhuaOuyang <15901283...@163.com> wrote: > > > Dear Mark, > >Thank you, I have figure out the problem, but to my surprise, the > output xpm file lack the information of the last residue for the CHARMM27 > force file (charmm's trajectory is good), but not for other force field. I > wonder whether the DSSP program in the gromacs ignore the last residue of > structures generated by CHARMM27 force field. > > Best regards, > Ouyang > > > > > > > > > At 2017-08-04 22:32:25, "Mark Abraham" wrote: > >Hi, > > > >Isn't that figure what is in the xpm file? > > > >Mark > > > >On Fri, Aug 4, 2017 at 4:20 PM YanhuaOuyang <15901283...@163.com> wrote: > > > >> Hi, > >>I have run a MD simulation and used gmx do_dssp to calculate the > >> secondary structure content. The output files are md_dssp.xpm and > >> scount.xvg. I want to know that each residue belongs to what kind of > >> secondary structure for each frame. But the scount.xvg output file only > >> have the number of residues with each secondary structure and the total > >> secondary structure count as a function of time. So, can I get the > >> information on "each residue belongs to which kind of secondary > structure > >> for each frame" to draw a figure of " amino acid vs secondary > structure" ? > >> > >> Best regards, > >> Ouyang > >> -- > >> 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] QSUB commands
Hi, This a question you should answer with the online documentation for your cluster. Mark On Sat, Aug 5, 2017 at 4:28 PM Neha Gupta wrote: > Hi gromacs users, > > I use cygwin terminal in windows 7, 64 bit computer. > > How to use qsub commands and thereby do gromacs simulations in a cluster? > > > > Can anyone tell me clearly? > > Thanks, > Neha > -- > 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] question about gmx do_dssp
On 8/5/17 8:12 PM, Mark Abraham wrote: Hi, I'd start by checking if that last residue is a normal one... The check_oo() function in gmx_do_dssp.cpp looks like it will not work correclty for CHARMM, because it does not identify CHARMM termini, thereby ignoring the C-terminus. It looks for O, O1, or OC1 (which actually doesn't appear to be used by any force field). CHARMM uses OT1/OT2 for COO- termini, so a check for OT1 needs to be added. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Generating topology file for a long polymer chain
On 8/5/17 8:12 AM, Mahsa E wrote: Dear gmx-users, I am trying to build a polymer box from scratch and generate the required input files. So far, I did these steps: 1. built a chain of the polymer 2. run ACPYPE to generate the topology file... However, since the chain is long, it took so long time with ACPYPE and the calculation is timed out without convergence. - Is it possible to restart the ACPYPE calculation? I read in some tutorials that it is also possible to run the ACPYPE calculations for the monomeric unit instead and repeat its parameters for the whole chain. How is it possible? The polymer chain may have a conformation with different angles and dihedrals than in the monomer. In general, how can I use the topology file of a monomer for the longer chain of a polymer ? Could you please advise me? You parametrize the monomer (charges, atom types, bonded parameters), then build up by doing, e.g. conformational energy scans of dihedral rotations between the dimer. That way you can build a proper model of the whole polymer. Do not try to parametrize an entire polymer at once; you'll end up with a conformation-specific solution for a given geometry, if you can even get it to work at all. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Gmx hbond
On 8/4/17 11:13 AM, farial tavakoli wrote:
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } Dear gromacs user
I am performing protein ligand complex (t4lysosim) and now i need to analyze JZ4 hydrogen bonding,
but when i type Gmx hbondThere is no JZ4 in the list to choose. It is because of i used :Gmx
make_ndx -f em.gro -o index.ndxAnd merged the " protein " and " JZ4" groupsIs
there anyone help me how to check the hydrogen bond of JZ4 ligand?
Both protein and ligand are default groups and do not require the use of an
index file. If the ligand isn't showing up in the list, it's probably because
you're supplying an index file from which the ligand group has been deleted.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
--
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Re: [gmx-users] Could not find clayff forcefield
On 8/4/17 4:57 AM, G R wrote: Dear users, I try to implement Clayff forcefield for Kaolinite. I created my force field (I'm not sure about it), but gromacs couldn't find my force field in the directory. Here is my forcefield. ffnonbonded [ atomtypes ] ; name mass chargeptype sigma eps HW 1 1.00800 0.4100A0.0e-01 0.0e-01 ;clayFF_waterhydrogen HO 1 1.00800 0.4250A0.0e-01 0.0e-01 ;clayFF_hydroxylhydrogen OW 8 15.99800-0.8200A3.16557e-01 6.50209e-01 ;ClayFF_wateroxygen OH 8 15.99800-0.9500A3.16557e-01 6.50209e-01 ;ClayFF_hydroxyloxygen OB 8 15.99800-1.0500A3.16557e-01 6.50209e-01 ;ClayFF_bridgingoxygen OBOS 8 15.99800-1.1808A3.16557e-01 6.50209e-01 ;ClayFF_bridgingoxygenoctasub OBTS 8 15.99800-1.1688A3.16557e-01 6.50209e-01 ;ClayFF_bridgingoxygentetrsub OHS 8 15.99800-1.0808A3.16557e-01 6.50209e-01 ;ClayFF_hydroxyloxygensub SI 14 28.08600 2.1000A3.30208e-01 8.0e-06 ;ClayFF_tetrahedralsilicon AO 13 26.98200 1.5750A4.27128e-01 6.0e-06 ;ClayFF_octahedalaluminium AT 13 26.98200 1.5750A3.30206e-01 8.0e-06 ;ClayFF_tetrasubaluminium ffbonded [ bondtypes ] ; ij func b0 kb OW HW 10.1000 554134.9 OH HO 10.1000 554134.9 OHSHO 10.1000 554134.9 [ angletypes ] ; ijk func th0 cth HW OWHW1109.47191.564 AL OHHO1109.47125.52 atomtype.n2t HHW0.4100 1.008 1O 0.100 ;water hydrogen OOW -0.820015.998 2H 0.100H 0.100 ;water oxygen OH2 OH -0.950015.998 1H 0.100 ;hydroxyl oxygen O2 obts -1.1688 15.998 0;bridging oxygen with tetrahedral substitution O1 obss -1.2996 15.998 0 ;bridging oxygen with double substitution OH1 ohs -1.0808 15.998 1 H 0.100 ;hydroxyl hydrogen with substitution Si st2.100028.086 0 ;tetrahedral silicon Al ao1.575026.982 0 ;octahedral aluminium Mg mgo1.360024.305 0 ; octahedral magnisium Na Na1.22.999 0 ;sodium ion forcefield.doc clayff.ff force field forcefield.itp #define _ff_clayff [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 3 yes 0.5 0.5 #include "ffnonbonded.itp" #include "ffbonded.itp" pdb Al0.6494.3333.377 Al3.248.8053.377 Al3.2032.8513.362 Al0.6397.3243.362 Si4.9623.0160.65 Si2.3987.4880.65 Si2.4421.470.653 Si-0.1225.9420.653 O1-0.3343.0982.268 O12.2587.572.268 O10.0415.8392.271 O12.6051.3672.271 O30.0144.4720 O3-1.8854.2597.154 O35.1694.4720 O33.274.2597.154 O32.57800 O30.678-0.2147.154 O32.6058.9450 O30.7068.7317.154 O31.0342.0560.177 O33.6266.5290.177 O31.0526.8480.023 O33.6162.3760.023 OH1-0.3228.6062.304 OH12.2424.1332.304 OH23.831.364.329 OH21.2665.8324.329 OH2-0.9624.1364.35 OH21.6298.6084.35 OH2-0.9617.5354.36 OH21.6023.0634.36 O22.63310.3122.271 OH23.85810.3054.329 OH24.8348.6062.304 OH24.1947.5354.36 O34.8213.0982.268 OH34.1934.1364.35 O36.192.0560.177 O3-1.5296.5290.177 It's to long, Sorry about it, but I really need to find out where is my problem. I put n2t file in directory not in my forcefield subdirectory. Do That's wrong. It needs to be in the force field subdirectory. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] The small organic molecule occurred deformation during simulation
On 8/4/17 4:42 AM, yujie liu wrote: Hello, users I’m a novice to study the gromacs program. Now I met some problems which the small molecule occurred deformation when energy minimization was performed. For example, the anthracene molecule became bent in the plane of C-rings, the same as phenol. I want to know whether the situation is normal? In addition, I employed gromos54a7.ff Slight out-of-plane distortions are possible because the rings aren't fully rigid. But if you're seeing significant distortion, it suggests your topology is wrong, likely due to missing or incorrect improper dihedrals, which serve to prevent out-of-plane deformation. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] The small organic molecule occurred deformation during simulation
-- 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] The small organic molecule occurred deformation during simulation
Mr Justin: I have tried to do energy minimization in this situation which only existing small molecule in water, I found the structure of organic molecule didn’t become distortions. I think the distortions of organic molecules are due to these stronger interactions between small molecules and enzyme, because there is a enzyme molecule in the previous simulation. Do you think this consideration is correct? In the case, do you think this phenomenon is normal? What’s more, I checked out the top file of small molecules and don’t find error and include the information of improper dihedrals. Thank you very much! Yours, Yujie liu -- 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] Continuing a run
Hi All, I had a crash in my system while running a simulation. After that, I used this command to continue: mdrun -s md_0_1.tpr -cpi md_0_1.cpt -append I had two .cpt files from the last simulation ( md_0_1.cpt and md_0_1_prev.cpt) and both were saved at the same time. So, I do not know whether I used the right .cpt file or not. At the end of the continuing run, I received new trajectory file which contains the small section of the rest of the simulation after the crash not whole the simulation, and it was not written on the last trajectory file (the last trajectory file remained unchanged). However, I used -append option to append the new output to the existing files. How can I append the new trajectory file to the last one to have a unique trajectory? By the way, I used Gromacs version 5.1.3 for the first simulation before the crash and 5.1.4 for after the crash. Kind regards,Mohammad -- 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] TOPOLOGY USING OPLS FORCEFIELD
Hi gromacs users, After getting the output from topolbuild, how to construct topology file using opls forcefield? Can anyone send useful links for the same? Thanks, Vidya.R -- 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.
