Re: [gmx-users] Pressure control with constraints incompatible with expanded ensemble
Hi, Jacob- Unfortunately, that is correct. We had though we'd have functionality that could support this combination in 2018 (a Monte Carlo barostat and/or expanded ensemble in alchemical space working with leapfrog), but those did not make it in. The support for MTTK with constraints was removed in order to simplify the inner loop of MD for other improvements. The good thing is that in virtually all situations at P near 1 atm, \Delta A and \Delta G for solvation calculations are pretty much identical, since P \Delta V is so smal. We can chat more if you think that you would need additional help on this. We are working with some improvements for expanded ensemble, so contact me off the list if you want to discuss those and see if they will help. We DO know for sure that expanded ensemble or replica exchange with Berendsen pressure control has some nasty issues (will be mentioned in a paper hopefully being submitted soon, so it's better documented). So don't do that. On Wed, Sep 5, 2018 at 12:54 PM Jacob Monroe wrote: > Hi all, > > I would like to use Gromacs (2018 versions on GPUs) to compute solvation > free energies using expanded ensemble simulations. I have no problems in > the NVT ensemble, but when I try and implement pressure control I run into > errors. > > Specifically, if I want to use expanded ensemble, I must use the md-vv > integrator. If I use this integrator, I must select MTTK pressure control > (I’d rather not use Berendsen for production runs), but if I want to > constrain hydrogen bonds, I cannot use MTTK (grompp throws an error). > Previous versions of Gromacs appear to have allowed MTTK as long as SHAKE > was used for constraints (see the mdp files here: > http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Ethanol_solvation_with_expanded_ensemble > ). > > So is the only way to run NPT, expanded ensemble simulations with current > versions of Gromacs to use the Berendsen barostat? > > Thanks, > Jacob > -- > 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: Adding new atom types
I'm not sure off the top of my head. The manual says: "Pair parameters that are not present in the [ pairtypes ] section are only generated when gen-pairs is set to “yes” in the [ defaults ] directive of forcefield.itp" so it sounds like the parameters in the [ pairtypes ] section should be kept if they are there. You could check this easily yourself by running a simple test case through grompp and seeing what is done. However, I should clarify/correct what I was wrote in my previous message as it wasn't 100 % correct (it's been a long week already!). Rather than [ nonbonded_params ] and [ pairtypes ] sections, I was actually referring to the link between the values given in the [ atomtypes ] and [ nonbonded_params ] sections of the GROMOS ffnonbonded.itp files. So this is where there are up to 3 different C12 values used to calculate the nonbonded_params for some atomtypes, as defined in the two tables I mentioned before in the linked paper. Because of the different C12 values, this is why you can't predict the [ nonbonded_params ] from the [ atomtypes ] using the standard combination rules. For the [ pairtypes ], you also can't predict some of these from the [ nonbonded_params ] sections (using fudgeLJ) because some of the atomtypes have explicit C6/C12 values to use just for 1-4 interactions (as given in table 9 of the paper I linked to), while others follow the fudgeLJ rule (i.e. are the same as those given in the [ nonbonded_params ] section). Because of this, you shouldn't try to generate the pairs for your new atomtype using gen-pairs but you should manually calculate and add them (as well as doing the same for the values in the [ nonbonded_params ] section). You should also be careful in doing these calculations because the C12 values given in the [ atomtypes ] section might not be the ones you want to use in the calculation of the nonbonded_params values for your new atomtype (even if your new atomtype only has one C12 value). That's because some of the atomtypes interact with themselves using the type 2 C12 values (e.g. atomtype OA), and so these are the values given for C12 in the [ atomtypes ] section Hopefully that all makes sense. Cheers Tom On 06/09/18 18:42, Alex wrote: Hi Tom, Thanks for the informative response. For the Gromos FF the gen-pairs is "no" and then the 1-4 interactions are taken from the parameters existed [ pairtypes ], if I change the gen-pairs to "yes" in Gromos FF, would you please confirm me that the parameters in [ pairtypes ] is still in privilege for those interactions whose parameters EXIST in the [ pairtypes ]? And if the parameters are not there they will be calculated by the fudgeLJ. Regards, Alex On Thu, Sep 6, 2018 at 10:58 AM Thomas Piggot wrote: The GROMOS force fields are somewhat different to the others in that they provide specific 1-4 interactions by having several different C12 parameters for one atomtype (in some cases). The C12 value used depends upon the atomtypes involved in the interactions (see tables 7 and 8 of https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20090 for more information for GROMOS 53A6). This means you cannot directly calculate the pairtypes from the nonbonded_params sections of the itp as you do not know what C12 value to use for the interaction. This also needs to be appropriately taken into account when adding a new atom type. You also need to explicitly add in the pairtypes, as by having multiple potential C12 parameters means it isn't possible to generate the pairtypes automatically. Cheers Tom On 06/09/18 15:27, Alex wrote: Dear all, Any idea please about my both questions below? The c6 in both [ nonbond_params ] to [ pairtypes ] comes from the combination rule of c6ij = (c6ii + c6jj)/2 but I could not find any rule about c12 in either sections! Thanks. Alex -- Forwarded message - From: Alex Date: Tue, Sep 4, 2018 at 2:43 PM Subject: Adding new atom types To: Hi all, Two questions on which your comments would be highly appreciated; 1. What is the difference between [ nonbond_params ] and [ pairtypes ] sections in ffnonbonded.itp file? For Gromos54a7 force filed with the "fudgeLJ = 1", I expected to have similar numbers for an the similar interactions when it is counted as [ nonbond_params ] or as [ pairtypes ] because of the scale = 1, but the "OE OA" interaction parameters change in [ nonbond_params ] to [ pairtypes ], similar story for the " OA O" interaction. Which is in contrast with my understanding of "fudgeLJ = 1". [ nonbond_params ] ; i j funcc6 c12 *OE OA 1 2.261954E-031.505529E-06* *OA O 1 2.261954E-031.386510E-06* [ pairtypes ] ; i j funcc6 c12 *OE OA 1 2.261954E-031.265625E-06* *OA O 1 2.261954E-039.687375E-07* 2. The gmx grompp gives some
[gmx-users] External sinusoidal force
Hi all, I asked this before and I think I remember the answer, so this is just to make sure, before we move to another software package. 1. We need a sinusoidal force of given direction, amplitude, and frequency applied to a selected group of atoms. Mimicking it with giving those atoms charge and applying an electric field is not an option. Is there absolutely anything else we can attempt? 2. Is this something I could request as a feature that could be implemented quickly (within weeks)? Same type of mdp syntax, except also input for the group. If it takes a while, makes no sense for us to wait, because LAMMPS can do it. The issue with LAMMPS is that it is ~5 times slower than Gromacs when using similar forcefields. 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.
[gmx-users] minimization is not converging (Bratin Kumar Das)
>> getting failed for my system Not clear to me. What are the errors? Did you passed all the steps. CHARMM-ui is quite robust. So if the initial structure of the protein and the pdb correctly formated and complete, CHARMM-GUI should work. Stéphane - Dear ABEL, I tried CHARMM-gui but the charmm gui is getting failed for my system. On Thu, Sep 6, 2018 at 8:50 PM, ABEL Stephane wrote: > Hi > > Did you try to use CHARMM-gui and use the gromacs files generated for this > system to see if your problem is resolved? > > St?phane > > -- > > Message: 5 > Date: Thu, 6 Sep 2018 19:55:07 +0530 > From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] minimization is not converging > Message-ID: > mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Thank you sir > > On Thu, Sep 6, 2018, 7:52 PM Justin Lemkul wrote: > > > > > > > On 9/6/18 10:09 AM, Bratin Kumar Das wrote: > > > Respected Dr. Justin > > > To avoid the complicacy I > solvated > > > only the protein pdb in a pbc box and tried for minimizatin. There also > > > minimization is not converging. Sir, till now I learned to carry out > > > protein ligand system md simulation successfully. I tried all possible > > ways > > > to simulate the my membrane protein system. I failed. Is it possible > that > > > the PDB file itself have some serious issue with its coordinates. the > > > structure refinement is required may be. > > > > It may, and I have already suggested a few things for you to check. > > Please do so. > > > > If you can provide more specific diagnostics of what is happening, > > someone on this list might be able to suggest something. What you've > > provided thus far is a generic instability that no one can diagnose. > > Investigate the structure, check for pdb2gmx warnings, follow the > > diagnostics I've already suggested, and report back with specific > > observations, a PDB code, and exact errors or warnings you get from any > > program if you need further help. > > > > -Justin > > > > -- > > == > > > > Justin A. Lemkul, Ph.D. > > Assistant Professor > > Virginia Tech Department of Biochemistry > > > > 303 Engel Hall > > 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. > > End of gromacs.org_gmx-users Digest, Vol 173, Issue 17 > ** > -- > 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. > -- Message: 4 Date: Thu, 6 Sep 2018 22:42:01 +0530 From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in> To: gmx-us...@gromacs.org Cc: "gromacs.org_gmx-users@maillist.sys.kth.se" Subject: Re: [gmx-users] minimization is not converging (Bratin Kumar Das) Message-ID: Content-Type: text/plain; charset="UTF-8" Dear ABEL, I tried CHARMM-gui but the charmm gui is getting failed for my system. On Thu, Sep 6, 2018 at 8:50 PM, ABEL Stephane wrote: > Hi > > Did you try to use CHARMM-gui and use the gromacs files generated for this > system to see if your problem is resolved? > > St?phane > > -- > > Message: 5 > Date: Thu, 6 Sep 2018 19:55:07 +0530 > From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] minimization is not converging > Message-ID: > mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Thank you sir > > On Thu, Sep 6, 2018, 7:52 PM Justin Lemkul wrote: > > > > > > > On 9/6/18 10:09
Re: [gmx-users] Fwd: Adding new atom types
Hi Tom, Thanks for the informative response. For the Gromos FF the gen-pairs is "no" and then the 1-4 interactions are taken from the parameters existed [ pairtypes ], if I change the gen-pairs to "yes" in Gromos FF, would you please confirm me that the parameters in [ pairtypes ] is still in privilege for those interactions whose parameters EXIST in the [ pairtypes ]? And if the parameters are not there they will be calculated by the fudgeLJ. Regards, Alex On Thu, Sep 6, 2018 at 10:58 AM Thomas Piggot wrote: > The GROMOS force fields are somewhat different to the others in that > they provide specific 1-4 interactions by having several different C12 > parameters for one atomtype (in some cases). The C12 value used depends > upon the atomtypes involved in the interactions (see tables 7 and 8 of > https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20090 for more > information for GROMOS 53A6). This means you cannot directly calculate > the pairtypes from the nonbonded_params sections of the itp as you do > not know what C12 value to use for the interaction. > > This also needs to be appropriately taken into account when adding a new > atom type. You also need to explicitly add in the pairtypes, as by > having multiple potential C12 parameters means it isn't possible to > generate the pairtypes automatically. > > Cheers > > Tom > > On 06/09/18 15:27, Alex wrote: > > Dear all, > > > > Any idea please about my both questions below? > > The c6 in both [ nonbond_params ] to [ pairtypes ] comes from the > > combination rule of c6ij = (c6ii + c6jj)/2 but I could not find any rule > > about c12 in either sections! > > > > Thanks. > > Alex > > > > > > -- Forwarded message - > > From: Alex > > Date: Tue, Sep 4, 2018 at 2:43 PM > > Subject: Adding new atom types > > To: > > > > > > Hi all, > > Two questions on which your comments would be highly appreciated; > > > > 1. What is the difference between [ nonbond_params ] and [ pairtypes ] > > sections in ffnonbonded.itp file? > > For Gromos54a7 force filed with the "fudgeLJ = 1", I expected to have > > similar numbers for an the similar interactions when it is counted as > > [ nonbond_params > > ] or as [ pairtypes ] because of the scale = 1, but the "OE OA" > interaction > > parameters change in [ nonbond_params ] to [ pairtypes ], similar story > > for the " OA O" interaction. Which is in contrast with my > > understanding of "fudgeLJ > > = 1". > > > > [ nonbond_params ] > > ; i j funcc6 c12 > > > > *OE OA 1 2.261954E-031.505529E-06* > > *OA O 1 2.261954E-031.386510E-06* > > > > [ pairtypes ] > > ; i j funcc6 c12 > > *OE OA 1 2.261954E-031.265625E-06* > > *OA O 1 2.261954E-039.687375E-07* > > > > 2. The gmx grompp gives some errors like; > > ERROR 1 [file topol.top, line ] > > No default LJ-14 types > > > > Which needs me to introduce new atom type ( of the problematic atoms) > > in atomtypes.atp > > and then in ffnonbonded.itp; > > Would you please confirm the procedure I should take to do so; > > First I have to add the atom type in atomtypes.atp: OC24 is an example; > > > > *echo "OC24 15.99940" >> atomtypes.atp* > > > > Then: > > *Adding "OC248 15.999400.00A > >0.0035644156892674973 6.222504156102231e-06" to > > the ffnonbonded.itp/[ atomtypes ]* > > > > Then: > > *Adding the "; i j funcc6 c12" for the OC24 > > in ffnonbonded.itp/[ nonbond_params ] and ffnonbonded.itp/[ pairtypes ]* > > > > Do I really need to edit the ffnonbonded.itp/[ nonbond_params ] and > > ffnonbonded.itp/[ pairtypes ] for the interactions of the new atom? or > the [ > > nonbond_params ] and [ pairtypes ] can be descided/governed by normal > > combination rule used in the FF, so that I do not need to put them in [ > > nonbond_params ] and ffnonbonded.itp/[ pairtypes ] > > > > Thanks. > > Alex > > -- > 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. > -- 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 is not converging (Bratin Kumar Das)
Dear ABEL, I tried CHARMM-gui but the charmm gui is getting failed for my system. On Thu, Sep 6, 2018 at 8:50 PM, ABEL Stephane wrote: > Hi > > Did you try to use CHARMM-gui and use the gromacs files generated for this > system to see if your problem is resolved? > > Stéphane > > -- > > Message: 5 > Date: Thu, 6 Sep 2018 19:55:07 +0530 > From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] minimization is not converging > Message-ID: > mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Thank you sir > > On Thu, Sep 6, 2018, 7:52 PM Justin Lemkul wrote: > > > > > > > On 9/6/18 10:09 AM, Bratin Kumar Das wrote: > > > Respected Dr. Justin > > > To avoid the complicacy I > solvated > > > only the protein pdb in a pbc box and tried for minimizatin. There also > > > minimization is not converging. Sir, till now I learned to carry out > > > protein ligand system md simulation successfully. I tried all possible > > ways > > > to simulate the my membrane protein system. I failed. Is it possible > that > > > the PDB file itself have some serious issue with its coordinates. the > > > structure refinement is required may be. > > > > It may, and I have already suggested a few things for you to check. > > Please do so. > > > > If you can provide more specific diagnostics of what is happening, > > someone on this list might be able to suggest something. What you've > > provided thus far is a generic instability that no one can diagnose. > > Investigate the structure, check for pdb2gmx warnings, follow the > > diagnostics I've already suggested, and report back with specific > > observations, a PDB code, and exact errors or warnings you get from any > > program if you need further help. > > > > -Justin > > > > -- > > == > > > > Justin A. Lemkul, Ph.D. > > Assistant Professor > > Virginia Tech Department of Biochemistry > > > > 303 Engel Hall > > 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. > > End of gromacs.org_gmx-users Digest, Vol 173, Issue 17 > ** > -- > 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] Workstation choice
Thank you, to use these tests isn’t a problem, but available workstation are too old, so test results won’t be helpful in choosing actual components. I have an access to high-performance cluster, but it also couldn’t be the basis because of its high cost. If it is hard to give the certain recommendation, I would to know at least how do performance correlate with the number of cores/threads and core frequency? What is more important the core frequency or number of cores? What is preferable, Intel or AMD? How should be correlated GPU and CPU performance? In the previous letters in mail-list I found recommendations on purchase of Threadripper 1950X+GeForce GTX-1080Ti, I think that more cheap and similar effective choice is TR 1950X+GeForce GTX-*1080*. Will there be significant differences with 1)TR 19*20*X+GeForce GTX-1080 2) Intel 7900x+GeForce GTX-1080? 2018-09-05 20:53 GMT+07:00 Benson Muite : > Hi Olga, > > The authors of: > > https://github.com/bio-phys/MDBenchmark/tree/version-1.3.2 > > https://zenodo.org/record/1318123 > > May be helpful. If your data is not confidential, you may consider running > Gromacs remotely on a cloud high performance computing resource, or > benchmarking remotely and then purchasing a suitable configuration. > > Some other information: > http://manual.gromacs.org/documentation/current/user-guide/ > mdrun-performance.html# > http://www.gromacs.org/GPU_acceleration > https://extras.csc.fi/chem/courses/gmx2007/Erik_Talks/buildi > ng_clusters.pdf > http://www.gromacs.org/Documentation/Performance_checklist > > On 09/05/2018 12:02 PM, Olga Selyutina wrote: > >> Hello, >> >> I need help in choice of the workstation for MD simulations using GROMACS. >> It is supposed to study systems consisting from 30-50k atoms, in >> particular, lipid bilayer models. Since the last generation of Intel and >> Ryzen CPU has made a big leap in performance, available workstation can’t >> be taken as a basis. Please, help to choose components of the workstation, >> particularly, GPU and CPU with total cost about $2000. What is better, to >> buy two GPUs(sli) or one GPU but more effective? >> >> > -- > 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. -- Best regards, Olga Selyutina -- 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] Functional Mode Analysis (FMA)
Hi Eduardo, The FMA tool is not yet included in the official distributed GROMACS version, but it is under code review. You can build GROMACS with the FMA tool from the attached tar ball of the development version that is currently being reviewed. The FMA tool can then be called as gmx fma (see gmx fma -h for options). The list doesn't accept attachments, so I sent you the tar ball off-list. Happy Computing, Thomas. -- R. Thomas Ullmann, PhD Theoretical & Computational Biophysics Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen, Germany thomas.ullm...@mpibpc.mpg.de www.bisb.uni-bayreuth.de/People/ullmannt -- -- 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] Functional Mode Analysis (FMA)
Hello! I'd like to know if the current version of gromacs has the fma tool, as described in this paper: * https://doi.org/10.1371/journal.pcbi.1000480 It is said in this page: http://www3.mpibpc.mpg.de/groups/de_groot/fma.html , that the fma tool should be included from version 5.1 onwards. Also in this page they say that one can use fma tool with gromacs version 4.0.7. As I don't know how to install this old version, I just used a bash script provided here: http://cmb.bio.uni-goettingen.de/fma.html . It installed successfully, but I don't know how to source the executables (in recent gromacs version I would only have to add source /usr/local/gromacs/bin/GMXRC on bash.rc) . Sorry if those a fool questions. Hope anyone can help me. Eduardo. -- 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 is not converging (Bratin Kumar Das)
Hi Did you try to use CHARMM-gui and use the gromacs files generated for this system to see if your problem is resolved? Stéphane -- Message: 5 Date: Thu, 6 Sep 2018 19:55:07 +0530 From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in> To: gmx-us...@gromacs.org Subject: Re: [gmx-users] minimization is not converging Message-ID: Content-Type: text/plain; charset="UTF-8" Thank you sir On Thu, Sep 6, 2018, 7:52 PM Justin Lemkul wrote: > > > On 9/6/18 10:09 AM, Bratin Kumar Das wrote: > > Respected Dr. Justin > > To avoid the complicacy I solvated > > only the protein pdb in a pbc box and tried for minimizatin. There also > > minimization is not converging. Sir, till now I learned to carry out > > protein ligand system md simulation successfully. I tried all possible > ways > > to simulate the my membrane protein system. I failed. Is it possible that > > the PDB file itself have some serious issue with its coordinates. the > > structure refinement is required may be. > > It may, and I have already suggested a few things for you to check. > Please do so. > > If you can provide more specific diagnostics of what is happening, > someone on this list might be able to suggest something. What you've > provided thus far is a generic instability that no one can diagnose. > Investigate the structure, check for pdb2gmx warnings, follow the > diagnostics I've already suggested, and report back with specific > observations, a PDB code, and exact errors or warnings you get from any > program if you need further help. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 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. End of gromacs.org_gmx-users Digest, Vol 173, Issue 17 ** -- 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] Warning: correlations not long enough
Dear All, In my simulations ,I have a Peptide in aqueous solution with a cosolvent. For more number of hydrogen bonds like peptide water, water-water, there are no warnings But for Peptide cosolvent, there are 315 hydrogen bonds and it does the acf as 315/315... It shows warning: correlations not long enough My original time step was 0.002 and I changed it to 0.0005 and even lowered the output frequency of coordinates Doing so gave me a 80GB output file! Still the problem persists.. The lifetime that is output on the screen is 45 ps. Since it writes that the lower half of the correlation function was fitted and then this is calculated, can I quote this lifetime? Is it accurate? Please help Yours sincerely Apramita -- 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] Hydrogen bond correlations do not start from 1
Dear All, Upon using the g_hbond command with -ac option to calculate forward lifetime,I see that the C(t) does not start from one and keeps varying for different systems like it starts from 0.8 or 0.6 etc... I have tried the normalize flag but to no avail. Will the lifetime output be reliable? This is for simulations that do not show any warning about the correlation time being not long enough. Please help Yours sincerely, Apramita -- 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: Adding new atom types
The GROMOS force fields are somewhat different to the others in that they provide specific 1-4 interactions by having several different C12 parameters for one atomtype (in some cases). The C12 value used depends upon the atomtypes involved in the interactions (see tables 7 and 8 of https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20090 for more information for GROMOS 53A6). This means you cannot directly calculate the pairtypes from the nonbonded_params sections of the itp as you do not know what C12 value to use for the interaction. This also needs to be appropriately taken into account when adding a new atom type. You also need to explicitly add in the pairtypes, as by having multiple potential C12 parameters means it isn't possible to generate the pairtypes automatically. Cheers Tom On 06/09/18 15:27, Alex wrote: Dear all, Any idea please about my both questions below? The c6 in both [ nonbond_params ] to [ pairtypes ] comes from the combination rule of c6ij = (c6ii + c6jj)/2 but I could not find any rule about c12 in either sections! Thanks. Alex -- Forwarded message - From: Alex Date: Tue, Sep 4, 2018 at 2:43 PM Subject: Adding new atom types To: Hi all, Two questions on which your comments would be highly appreciated; 1. What is the difference between [ nonbond_params ] and [ pairtypes ] sections in ffnonbonded.itp file? For Gromos54a7 force filed with the "fudgeLJ = 1", I expected to have similar numbers for an the similar interactions when it is counted as [ nonbond_params ] or as [ pairtypes ] because of the scale = 1, but the "OE OA" interaction parameters change in [ nonbond_params ] to [ pairtypes ], similar story for the " OA O" interaction. Which is in contrast with my understanding of "fudgeLJ = 1". [ nonbond_params ] ; i j funcc6 c12 *OE OA 1 2.261954E-031.505529E-06* *OA O 1 2.261954E-031.386510E-06* [ pairtypes ] ; i j funcc6 c12 *OE OA 1 2.261954E-031.265625E-06* *OA O 1 2.261954E-039.687375E-07* 2. The gmx grompp gives some errors like; ERROR 1 [file topol.top, line ] No default LJ-14 types Which needs me to introduce new atom type ( of the problematic atoms) in atomtypes.atp and then in ffnonbonded.itp; Would you please confirm the procedure I should take to do so; First I have to add the atom type in atomtypes.atp: OC24 is an example; *echo "OC24 15.99940" >> atomtypes.atp* Then: *Adding "OC248 15.999400.00A 0.0035644156892674973 6.222504156102231e-06" to the ffnonbonded.itp/[ atomtypes ]* Then: *Adding the "; i j funcc6 c12" for the OC24 in ffnonbonded.itp/[ nonbond_params ] and ffnonbonded.itp/[ pairtypes ]* Do I really need to edit the ffnonbonded.itp/[ nonbond_params ] and ffnonbonded.itp/[ pairtypes ] for the interactions of the new atom? or the [ nonbond_params ] and [ pairtypes ] can be descided/governed by normal combination rule used in the FF, so that I do not need to put them in [ nonbond_params ] and ffnonbonded.itp/[ pairtypes ] Thanks. Alex -- 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] Fwd: Adding new atom types
Dear all, Any idea please about my both questions below? The c6 in both [ nonbond_params ] to [ pairtypes ] comes from the combination rule of c6ij = (c6ii + c6jj)/2 but I could not find any rule about c12 in either sections! Thanks. Alex -- Forwarded message - From: Alex Date: Tue, Sep 4, 2018 at 2:43 PM Subject: Adding new atom types To: Hi all, Two questions on which your comments would be highly appreciated; 1. What is the difference between [ nonbond_params ] and [ pairtypes ] sections in ffnonbonded.itp file? For Gromos54a7 force filed with the "fudgeLJ = 1", I expected to have similar numbers for an the similar interactions when it is counted as [ nonbond_params ] or as [ pairtypes ] because of the scale = 1, but the "OE OA" interaction parameters change in [ nonbond_params ] to [ pairtypes ], similar story for the " OA O" interaction. Which is in contrast with my understanding of "fudgeLJ = 1". [ nonbond_params ] ; i j funcc6 c12 *OE OA 1 2.261954E-031.505529E-06* *OA O 1 2.261954E-031.386510E-06* [ pairtypes ] ; i j funcc6 c12 *OE OA 1 2.261954E-031.265625E-06* *OA O 1 2.261954E-039.687375E-07* 2. The gmx grompp gives some errors like; ERROR 1 [file topol.top, line ] No default LJ-14 types Which needs me to introduce new atom type ( of the problematic atoms) in atomtypes.atp and then in ffnonbonded.itp; Would you please confirm the procedure I should take to do so; First I have to add the atom type in atomtypes.atp: OC24 is an example; *echo "OC24 15.99940" >> atomtypes.atp* Then: *Adding "OC248 15.999400.00A 0.0035644156892674973 6.222504156102231e-06" to the ffnonbonded.itp/[ atomtypes ]* Then: *Adding the "; i j funcc6 c12" for the OC24 in ffnonbonded.itp/[ nonbond_params ] and ffnonbonded.itp/[ pairtypes ]* Do I really need to edit the ffnonbonded.itp/[ nonbond_params ] and ffnonbonded.itp/[ pairtypes ] for the interactions of the new atom? or the [ nonbond_params ] and [ pairtypes ] can be descided/governed by normal combination rule used in the FF, so that I do not need to put them in [ nonbond_params ] and ffnonbonded.itp/[ pairtypes ] Thanks. 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.
Re: [gmx-users] minimization is not converging
Thank you sir On Thu, Sep 6, 2018, 7:52 PM Justin Lemkul wrote: > > > On 9/6/18 10:09 AM, Bratin Kumar Das wrote: > > Respected Dr. Justin > > To avoid the complicacy I solvated > > only the protein pdb in a pbc box and tried for minimizatin. There also > > minimization is not converging. Sir, till now I learned to carry out > > protein ligand system md simulation successfully. I tried all possible > ways > > to simulate the my membrane protein system. I failed. Is it possible that > > the PDB file itself have some serious issue with its coordinates. the > > structure refinement is required may be. > > It may, and I have already suggested a few things for you to check. > Please do so. > > If you can provide more specific diagnostics of what is happening, > someone on this list might be able to suggest something. What you've > provided thus far is a generic instability that no one can diagnose. > Investigate the structure, check for pdb2gmx warnings, follow the > diagnostics I've already suggested, and report back with specific > observations, a PDB code, and exact errors or warnings you get from any > program if you need further help. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 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] minimization is not converging
On 9/6/18 10:09 AM, Bratin Kumar Das wrote: Respected Dr. Justin To avoid the complicacy I solvated only the protein pdb in a pbc box and tried for minimizatin. There also minimization is not converging. Sir, till now I learned to carry out protein ligand system md simulation successfully. I tried all possible ways to simulate the my membrane protein system. I failed. Is it possible that the PDB file itself have some serious issue with its coordinates. the structure refinement is required may be. It may, and I have already suggested a few things for you to check. Please do so. If you can provide more specific diagnostics of what is happening, someone on this list might be able to suggest something. What you've provided thus far is a generic instability that no one can diagnose. Investigate the structure, check for pdb2gmx warnings, follow the diagnostics I've already suggested, and report back with specific observations, a PDB code, and exact errors or warnings you get from any program if you need further help. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 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.
Re: [gmx-users] minimization is not converging
Respected Dr. Justin To avoid the complicacy I solvated only the protein pdb in a pbc box and tried for minimizatin. There also minimization is not converging. Sir, till now I learned to carry out protein ligand system md simulation successfully. I tried all possible ways to simulate the my membrane protein system. I failed. Is it possible that the PDB file itself have some serious issue with its coordinates. the structure refinement is required may be. On Thu, Sep 6, 2018, 7:24 PM Justin Lemkul wrote: > > > On 9/6/18 9:51 AM, Bratin Kumar Das wrote: > > Respected Dr Justin, > > I took one membrane protein pdb > file > > and converted it to .gro using pdb2gmx. Next I builded and packed the > POPC > > phospholipids bylayer using vmd membrane builder plugin. Subsequently I > > solvated the system in vmd only. The entire system was converted to .gro > > and all the water molecules and POPC molecules making bad contacts are > > deleted. I added ions to nutralize the system in gromacs using genion. > > Prior to that all the POPC topoloy properly included in topol.top. prior > to > > energy minimization all the steps ran with out fatal error. I followed > the > > procidure explained in gromacs tutorial. Evrey cases the same error is > > coming during minimization. > > It's not worth moving on to a complicated membrane system when you said > the protein itself does not minimize properly. Solve the easier problem > first and work with just the protein. Only when you understand why that > was unstable should you move on to the membrane system. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 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. > On Sep 6, 2018 7:24 PM, "Justin Lemkul" wrote: On 9/6/18 9:51 AM, Bratin Kumar Das wrote: > Respected Dr Justin, > I took one membrane protein pdb file > and converted it to .gro using pdb2gmx. Next I builded and packed the POPC > phospholipids bylayer using vmd membrane builder plugin. Subsequently I > solvated the system in vmd only. The entire system was converted to .gro > and all the water molecules and POPC molecules making bad contacts are > deleted. I added ions to nutralize the system in gromacs using genion. > Prior to that all the POPC topoloy properly included in topol.top. prior to > energy minimization all the steps ran with out fatal error. I followed the > procidure explained in gromacs tutorial. Evrey cases the same error is > coming during minimization. It's not worth moving on to a complicated membrane system when you said the protein itself does not minimize properly. Solve the easier problem first and work with just the protein. Only when you understand why that was unstable should you move on to the membrane system. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 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] minimization is not converging
On 9/6/18 9:51 AM, Bratin Kumar Das wrote: Respected Dr Justin, I took one membrane protein pdb file and converted it to .gro using pdb2gmx. Next I builded and packed the POPC phospholipids bylayer using vmd membrane builder plugin. Subsequently I solvated the system in vmd only. The entire system was converted to .gro and all the water molecules and POPC molecules making bad contacts are deleted. I added ions to nutralize the system in gromacs using genion. Prior to that all the POPC topoloy properly included in topol.top. prior to energy minimization all the steps ran with out fatal error. I followed the procidure explained in gromacs tutorial. Evrey cases the same error is coming during minimization. It's not worth moving on to a complicated membrane system when you said the protein itself does not minimize properly. Solve the easier problem first and work with just the protein. Only when you understand why that was unstable should you move on to the membrane system. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 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.
Re: [gmx-users] minimization is not converging
Respected Dr Justin, I took one membrane protein pdb file and converted it to .gro using pdb2gmx. Next I builded and packed the POPC phospholipids bylayer using vmd membrane builder plugin. Subsequently I solvated the system in vmd only. The entire system was converted to .gro and all the water molecules and POPC molecules making bad contacts are deleted. I added ions to nutralize the system in gromacs using genion. Prior to that all the POPC topoloy properly included in topol.top. prior to energy minimization all the steps ran with out fatal error. I followed the procidure explained in gromacs tutorial. Evrey cases the same error is coming during minimization. On Thu, Sep 6, 2018, 7:06 PM Justin Lemkul wrote: > > > On 9/6/18 9:34 AM, Bratin Kumar Das wrote: > > Respected Dr Justin, > >In pdb2gmx command i used -ignh > flag > > to ignore the hydrogens. Previously with out using this flag gave missing > > atom error. May be some hydrogens were missed. Is it possible that the > > error happening due to the flag (ignh). > > No, because that's not what -ignh does. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 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] minimization is not converging
On 9/6/18 9:34 AM, Bratin Kumar Das wrote: Respected Dr Justin, In pdb2gmx command i used -ignh flag to ignore the hydrogens. Previously with out using this flag gave missing atom error. May be some hydrogens were missed. Is it possible that the error happening due to the flag (ignh). No, because that's not what -ignh does. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 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.
Re: [gmx-users] minimization is not converging
Respected Dr Justin, In pdb2gmx command i used -ignh flag to ignore the hydrogens. Previously with out using this flag gave missing atom error. May be some hydrogens were missed. Is it possible that the error happening due to the flag (ignh). On Thu, Sep 6, 2018, 5:42 PM Justin Lemkul wrote: > > > On 9/6/18 8:04 AM, Bratin Kumar Das wrote: > > Respected Dr. Justin, > >Thanking you for your valuable advice. > > Actually, I also tried to minimised the protein alone in the solvent > > without the membrane. so, result was similar. The system bowed up > > similarly. Is it possible that due to inherent problem in topology this > > phenomena is happening. > > Yes, but any sensible protein structure will not have such issues. Make > sure you haven't ignored warnings from pdb2gmx about missing residues, > long bonds, etc. that indicate problems with the structure. And again, > look at the mdrun output - it tells you where the largest forces are, > which is usually right where the problem is. > > -Justin > > > On Thu, Sep 6, 2018 at 5:20 PM, Justin Lemkul wrote: > > > >> > >> On 9/6/18 7:47 AM, Bratin Kumar Das wrote: > >> > >>> Dear all, > >>>I am running a membrane simulation with GCGR protein. I > am > >>> getting the following warning and error > >>> > >> Your system is unstable and blowing up. mdrun is telling you something > is > >> really bad around atom 15058, so start looking there and follow advice > at: > >> http://www.gromacs.org/Documentation/Terminology/Blowing_Up# > >> Diagnosing_an_Unstable_System > >> > >> -Justin > >> > >> > >> gmx mdrun -v -s em_1.tpr -deffnm em_1 > >>> :-) GROMACS - gmx mdrun, 2016.5 (-: > >>> > >>> GROMACS is written by: > >>>Emile Apol Rossen Apostolov Herman J.C. BerendsenPar > >>> Bjelkmar > >>>Aldert van Buuren Rudi van Drunen Anton FeenstraGerrit > >>> Groenhof > >>>Christoph Junghans Anca HamuraruVincent Hindriksen Dimitrios > >>> Karkoulis > >>> Peter KassonJiri Kraus Carsten Kutzner Per > Larsson > >>> Justin A. Lemkul Magnus Lundborg Pieter MeulenhoffErik > Marklund > >>> Teemu Murtola Szilard Pall Sander Pronk Roland > Schulz > >>> Alexey Shvetsov Michael Shirts Alfons Sijbers Peter > >>> Tieleman > >>> Teemu Virolainen Christian WennbergMaarten Wolf > >>> and the project leaders: > >>> Mark Abraham, Berk Hess, Erik Lindahl, and David van der > Spoel > >>> > >>> Copyright (c) 1991-2000, University of Groningen, The Netherlands. > >>> Copyright (c) 2001-2017, The GROMACS development team at > >>> Uppsala University, Stockholm University and > >>> the Royal Institute of Technology, Sweden. > >>> check out http://www.gromacs.org for more information. > >>> > >>> GROMACS is free software; you can redistribute it and/or modify it > >>> under the terms of the GNU Lesser General Public License > >>> as published by the Free Software Foundation; either version 2.1 > >>> of the License, or (at your option) any later version. > >>> > >>> GROMACS: gmx mdrun, version 2016.5 > >>> Executable: /usr/local/gromacs/bin/gmx > >>> Data prefix: /usr/local/gromacs > >>> Working dir: /home/workstation/Documents/GR > >>> OMACS_projects/GROMACS_GCGR_new > >>> Command line: > >>> gmx mdrun -v -s em_1.tpr -deffnm em_1 > >>> > >>> > >>> Running on 1 node with total 4 cores, 4 logical cores > >>> Hardware detected: > >>> CPU info: > >>> Vendor: Intel > >>> Brand: Intel(R) Xeon(R) CPU E3-1225 v5 @ 3.30GHz > >>> SIMD instructions most likely to fit this hardware: AVX2_256 > >>> SIMD instructions selected at GROMACS compile time: AVX2_256 > >>> > >>> Hardware topology: Basic > >>> > >>> Reading file em_1.tpr, VERSION 2016.5 (single precision) > >>> Using 1 MPI thread > >>> Using 4 OpenMP threads > >>> > >>> > >>> Steepest Descents: > >>> Tolerance (Fmax) = 1.0e+01 > >>> Number of steps= 2000 > >>> > >>> WARNING: Listed nonbonded interaction between particles 19562 and 19566 > >>> at distance 2.420 which is larger than the table limit 2.200 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. > >>> > >>> > >>> > >>> WARNING: Listed nonbonded
Re: [gmx-users] minimization is not converging
On 9/6/18 8:04 AM, Bratin Kumar Das wrote: Respected Dr. Justin, Thanking you for your valuable advice. Actually, I also tried to minimised the protein alone in the solvent without the membrane. so, result was similar. The system bowed up similarly. Is it possible that due to inherent problem in topology this phenomena is happening. Yes, but any sensible protein structure will not have such issues. Make sure you haven't ignored warnings from pdb2gmx about missing residues, long bonds, etc. that indicate problems with the structure. And again, look at the mdrun output - it tells you where the largest forces are, which is usually right where the problem is. -Justin On Thu, Sep 6, 2018 at 5:20 PM, Justin Lemkul wrote: On 9/6/18 7:47 AM, Bratin Kumar Das wrote: Dear all, I am running a membrane simulation with GCGR protein. I am getting the following warning and error Your system is unstable and blowing up. mdrun is telling you something is really bad around atom 15058, so start looking there and follow advice at: http://www.gromacs.org/Documentation/Terminology/Blowing_Up# Diagnosing_an_Unstable_System -Justin gmx mdrun -v -s em_1.tpr -deffnm em_1 :-) GROMACS - gmx mdrun, 2016.5 (-: GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. BerendsenPar Bjelkmar Aldert van Buuren Rudi van Drunen Anton FeenstraGerrit Groenhof Christoph Junghans Anca HamuraruVincent Hindriksen Dimitrios Karkoulis Peter KassonJiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Magnus Lundborg Pieter MeulenhoffErik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen Christian WennbergMaarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2017, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2016.5 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /home/workstation/Documents/GR OMACS_projects/GROMACS_GCGR_new Command line: gmx mdrun -v -s em_1.tpr -deffnm em_1 Running on 1 node with total 4 cores, 4 logical cores Hardware detected: CPU info: Vendor: Intel Brand: Intel(R) Xeon(R) CPU E3-1225 v5 @ 3.30GHz SIMD instructions most likely to fit this hardware: AVX2_256 SIMD instructions selected at GROMACS compile time: AVX2_256 Hardware topology: Basic Reading file em_1.tpr, VERSION 2016.5 (single precision) Using 1 MPI thread Using 4 OpenMP threads Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps= 2000 WARNING: Listed nonbonded interaction between particles 19562 and 19566 at distance 2.420 which is larger than the table limit 2.200 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. WARNING: Listed nonbonded interaction between particles 9914 and 9918 at distance 2.232 which is larger than the table limit 2.200 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. WARNING: Listed nonbonded interaction between particles 29342 and 29348 at distance 2.250 which is larger than the table limit 2.200 nm. This is likely either a 1,4 interaction, or a listed interaction inside
Re: [gmx-users] minimization is not converging
Respected Dr. Justin, Thanking you for your valuable advice. Actually, I also tried to minimised the protein alone in the solvent without the membrane. so, result was similar. The system bowed up similarly. Is it possible that due to inherent problem in topology this phenomena is happening. On Thu, Sep 6, 2018 at 5:20 PM, Justin Lemkul wrote: > > > On 9/6/18 7:47 AM, Bratin Kumar Das wrote: > >> Dear all, >> I am running a membrane simulation with GCGR protein. I am >> getting the following warning and error >> > > Your system is unstable and blowing up. mdrun is telling you something is > really bad around atom 15058, so start looking there and follow advice at: > http://www.gromacs.org/Documentation/Terminology/Blowing_Up# > Diagnosing_an_Unstable_System > > -Justin > > > gmx mdrun -v -s em_1.tpr -deffnm em_1 >>:-) GROMACS - gmx mdrun, 2016.5 (-: >> >> GROMACS is written by: >> Emile Apol Rossen Apostolov Herman J.C. BerendsenPar >> Bjelkmar >> Aldert van Buuren Rudi van Drunen Anton FeenstraGerrit >> Groenhof >> Christoph Junghans Anca HamuraruVincent Hindriksen Dimitrios >> Karkoulis >> Peter KassonJiri Kraus Carsten Kutzner Per Larsson >>Justin A. Lemkul Magnus Lundborg Pieter MeulenhoffErik Marklund >> Teemu Murtola Szilard Pall Sander Pronk Roland Schulz >>Alexey Shvetsov Michael Shirts Alfons Sijbers Peter >> Tieleman >>Teemu Virolainen Christian WennbergMaarten Wolf >> and the project leaders: >> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel >> >> Copyright (c) 1991-2000, University of Groningen, The Netherlands. >> Copyright (c) 2001-2017, The GROMACS development team at >> Uppsala University, Stockholm University and >> the Royal Institute of Technology, Sweden. >> check out http://www.gromacs.org for more information. >> >> GROMACS is free software; you can redistribute it and/or modify it >> under the terms of the GNU Lesser General Public License >> as published by the Free Software Foundation; either version 2.1 >> of the License, or (at your option) any later version. >> >> GROMACS: gmx mdrun, version 2016.5 >> Executable: /usr/local/gromacs/bin/gmx >> Data prefix: /usr/local/gromacs >> Working dir: /home/workstation/Documents/GR >> OMACS_projects/GROMACS_GCGR_new >> Command line: >>gmx mdrun -v -s em_1.tpr -deffnm em_1 >> >> >> Running on 1 node with total 4 cores, 4 logical cores >> Hardware detected: >>CPU info: >> Vendor: Intel >> Brand: Intel(R) Xeon(R) CPU E3-1225 v5 @ 3.30GHz >> SIMD instructions most likely to fit this hardware: AVX2_256 >> SIMD instructions selected at GROMACS compile time: AVX2_256 >> >>Hardware topology: Basic >> >> Reading file em_1.tpr, VERSION 2016.5 (single precision) >> Using 1 MPI thread >> Using 4 OpenMP threads >> >> >> Steepest Descents: >> Tolerance (Fmax) = 1.0e+01 >> Number of steps= 2000 >> >> WARNING: Listed nonbonded interaction between particles 19562 and 19566 >> at distance 2.420 which is larger than the table limit 2.200 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. >> >> >> >> WARNING: Listed nonbonded interaction between particles 9914 and 9918 >> at distance 2.232 which is larger than the table limit 2.200 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. >> >> >> >> WARNING: Listed nonbonded interaction between particles 29342 and 29348 >> at distance 2.250 which is larger than the table limit 2.200 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
Re: [gmx-users] Justin paper 2010 pulling
On 9/6/18 2:29 AM, Rakesh Mishra wrote: While I have purely physics background. But, In my thinking, there are hydrogen bonds (electrostatic attractive interaction) between bp of both the strands of DNA/RNA which are perpendicular to helix direction. And the other thing you have chosen very fast velocity like (0.01, 0.001, 0.005 ). This can also be the reason of smoothness. But can you tell me one thing please,the value of spring constant of biasing that you have taken (k= 1000), is standard or not . If this value can be taken for peptide pulling . Can this value of spring constant (k=1000) can be taken for DNA (or dna+drug) pulling or not . There is no such thing as a "standard" force constant for pulling. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 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.
Re: [gmx-users] minimization is not converging
On 9/6/18 7:47 AM, Bratin Kumar Das wrote: Dear all, I am running a membrane simulation with GCGR protein. I am getting the following warning and error Your system is unstable and blowing up. mdrun is telling you something is really bad around atom 15058, so start looking there and follow advice at: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System -Justin gmx mdrun -v -s em_1.tpr -deffnm em_1 :-) GROMACS - gmx mdrun, 2016.5 (-: GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. BerendsenPar Bjelkmar Aldert van Buuren Rudi van Drunen Anton FeenstraGerrit Groenhof Christoph Junghans Anca HamuraruVincent Hindriksen Dimitrios Karkoulis Peter KassonJiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Magnus Lundborg Pieter MeulenhoffErik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen Christian WennbergMaarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2017, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2016.5 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /home/workstation/Documents/GROMACS_projects/GROMACS_GCGR_new Command line: gmx mdrun -v -s em_1.tpr -deffnm em_1 Running on 1 node with total 4 cores, 4 logical cores Hardware detected: CPU info: Vendor: Intel Brand: Intel(R) Xeon(R) CPU E3-1225 v5 @ 3.30GHz SIMD instructions most likely to fit this hardware: AVX2_256 SIMD instructions selected at GROMACS compile time: AVX2_256 Hardware topology: Basic Reading file em_1.tpr, VERSION 2016.5 (single precision) Using 1 MPI thread Using 4 OpenMP threads Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps= 2000 WARNING: Listed nonbonded interaction between particles 19562 and 19566 at distance 2.420 which is larger than the table limit 2.200 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. WARNING: Listed nonbonded interaction between particles 9914 and 9918 at distance 2.232 which is larger than the table limit 2.200 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. WARNING: Listed nonbonded interaction between particles 29342 and 29348 at distance 2.250 which is larger than the table limit 2.200 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. Step=0, Dmax= 1.0e-02 nm, Epot= 1.42935e+20 Fmax= inf, atom= 15058 Step=1, Dmax= 1.0e-02 nm, Epot= 1.42929e+20 Fmax= inf, atom= 15058 Step= 15, Dmax= 1.5e-06 nm, Epot= 1.42941e+20 Fmax= inf, atom= 15058 Energy minimization has stopped, but the forces have not
[gmx-users] minimization is not converging
Dear all, I am running a membrane simulation with GCGR protein. I am getting the following warning and error gmx mdrun -v -s em_1.tpr -deffnm em_1 :-) GROMACS - gmx mdrun, 2016.5 (-: GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. BerendsenPar Bjelkmar Aldert van Buuren Rudi van Drunen Anton FeenstraGerrit Groenhof Christoph Junghans Anca HamuraruVincent Hindriksen Dimitrios Karkoulis Peter KassonJiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Magnus Lundborg Pieter MeulenhoffErik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen Christian WennbergMaarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2017, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2016.5 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /home/workstation/Documents/GROMACS_projects/GROMACS_GCGR_new Command line: gmx mdrun -v -s em_1.tpr -deffnm em_1 Running on 1 node with total 4 cores, 4 logical cores Hardware detected: CPU info: Vendor: Intel Brand: Intel(R) Xeon(R) CPU E3-1225 v5 @ 3.30GHz SIMD instructions most likely to fit this hardware: AVX2_256 SIMD instructions selected at GROMACS compile time: AVX2_256 Hardware topology: Basic Reading file em_1.tpr, VERSION 2016.5 (single precision) Using 1 MPI thread Using 4 OpenMP threads Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps= 2000 WARNING: Listed nonbonded interaction between particles 19562 and 19566 at distance 2.420 which is larger than the table limit 2.200 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. WARNING: Listed nonbonded interaction between particles 9914 and 9918 at distance 2.232 which is larger than the table limit 2.200 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. WARNING: Listed nonbonded interaction between particles 29342 and 29348 at distance 2.250 which is larger than the table limit 2.200 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. Step=0, Dmax= 1.0e-02 nm, Epot= 1.42935e+20 Fmax= inf, atom= 15058 Step=1, Dmax= 1.0e-02 nm, Epot= 1.42929e+20 Fmax= inf, atom= 15058 Step= 15, Dmax= 1.5e-06 nm, Epot= 1.42941e+20 Fmax= inf, atom= 15058 Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 10 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision,
Re: [gmx-users] Orthorhombic structure and Lincs warnings
Your answers to questions 3 and 4 contradict each other in several ways. Do not use restraints or constraints (hint: LINCS is a constraint algorithm) and make sure your forcefield works. Right now it doesn't work, because a somewhat working forcefield does not lead to any crumpling, i.e. fix it and use appropriately selected box dimensions, especially if you are using periodic boundaries. This is a searchable list and people asked the very same questions before. If your box is rectangular, there is no need to call it orthorhombic. In your QM calculations, if you have a rectangular sheet of graphene with boundaries parallel & perpendicular to the vector connecting the atoms in the unit cell, the in-plane vectors of the cell must be 90 degrees, so there goes the accuracy of your quantum espresso setup. And please, please respond in the appropriate thread. There is absolutely no need to flood the entire mailing list, now including the digest. Alex On 9/6/2018 12:48 AM, sagar bathla wrote: Hi Alex , sorry to post my problem too many times. Coming back to your questions related to my problem 1. angles are 90,90,120 in x,y and z respectively. actually in quantum espresso this structure is little bit easy to handle. 2. without LINCS i haven't tried the simulation, i will do it without LINCS and get back to you. 3. I am basically interested in dynamics of water through porous graphene. if i am not using constraint and all it is getting crumbled and shape of graphene changes. 4. Yes, it is stable. 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] gromacs.org_gmx-users Digest, Vol 173, Issue 12
Hi Alex , sorry to post my problem too many times. Coming back to your questions related to my problem 1. angles are 90,90,120 in x,y and z respectively. actually in quantum espresso this structure is little bit easy to handle. 2. without LINCS i haven't tried the simulation, i will do it without LINCS and get back to you. 3. I am basically interested in dynamics of water through porous graphene. if i am not using constraint and all it is getting crumbled and shape of graphene changes. 4. Yes, it is stable. Regards On Thu, Sep 6, 2018 at 5:35 AM < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > 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. Orthorhombic structure and Lincs warnings (sagar bathla) >2. Re: Orthorhombic structure and Lincs warnings (Alex) >3. Re: Orthorhombic structure and Lincs warnings (Alex) >4. Re: Justin paper 2010 pulling (Justin Lemkul) >5. Re: i have a question about multiple chain simulation at the > same box (Justin Lemkul) > > > -- > > Message: 1 > Date: Thu, 6 Sep 2018 01:05:03 +0530 > From: sagar bathla > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] Orthorhombic structure and Lincs warnings > Message-ID: > < > caexvse4c4pjpun0nsnycsdj33ge6vlfysbbxe8w+hmaky9q...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Dear all, > > Can simulation for orthorhombic structure be done in gromacs? > Actually I am working with 2-D graphene sheets which are like a > parallelogram. > > In my system, there is a graphene sheet (restrained)and water. > After the energy minimization, energy is coming positive (order of 10^8) > On Visualization in vmd, the structure appears to be rectangle and there > comes a warning with it > > 152 inconsistant shifts etc. > > When I am trying to equillibrate the system then so many lines warnings > appears of rotation of bonds more than 90 degrees and simulation crashes > everytime. > > Is there any problem with structure or y else? > Earlier also I posted this but issue hasn't resolved yet. > > Please help me to find this problem. > > Regards > Sagar > > > -- > > Message: 2 > Date: Wed, 5 Sep 2018 13:45:34 -0600 > From: Alex > To: Discussion list for GROMACS users > Cc: Discussion list for GROMACS users > > Subject: Re: [gmx-users] Orthorhombic structure and Lincs warnings > Message-ID: > < > camjz6qhx-fnmnqxgeoypz22cq4yrvn8eynddhfqpyfg1kym...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > It's not the first time you're posting this message and there's a reason > noone is replying. > > 1. What are the inter-axis angles of that orthorhombic box? Why not a > rectangular box? > 2. Why are you using LINCS with graphene, which should _not_ be simulated > with constraints? > 3. Why are you restraining your system on top of everything else? > 4. Did you verify that your graphene model (without constraints or > restraints) was stable prior to adding water? > > Alex > > On Wed, Sep 5, 2018 at 1:35 PM sagar bathla > wrote: > > > Dear all, > > > > Can simulation for orthorhombic structure be done in gromacs? > > Actually I am working with 2-D graphene sheets which are like a > > parallelogram. > > > > In my system, there is a graphene sheet (restrained)and water. > > After the energy minimization, energy is coming positive (order of 10^8) > > On Visualization in vmd, the structure appears to be rectangle and there > > comes a warning with it > > > > 152 inconsistant shifts etc. > > > > When I am trying to equillibrate the system then so many lines warnings > > appears of rotation of bonds more than 90 degrees and simulation crashes > > everytime. > > > > Is there any problem with structure or y else? > > Earlier also I posted this but issue hasn't resolved yet. > > > > Please help me to find this problem. > > > > Regards > > Sagar > > -- > > 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. > > > > > -- > > Message: 3
Re: [gmx-users] Justin paper 2010 pulling
While I have purely physics background. But, In my thinking, there are hydrogen bonds (electrostatic attractive interaction) between bp of both the strands of DNA/RNA which are perpendicular to helix direction. And the other thing you have chosen very fast velocity like (0.01, 0.001, 0.005 ). This can also be the reason of smoothness. But can you tell me one thing please,the value of spring constant of biasing that you have taken (k= 1000), is standard or not . If this value can be taken for peptide pulling . Can this value of spring constant (k=1000) can be taken for DNA (or dna+drug) pulling or not . On Thu, Sep 6, 2018 at 5:31 AM, Justin Lemkul wrote: > > > On 9/5/18 1:50 AM, Rakesh Mishra wrote: > >> So that means >> >> It is may be due to the difference in the type of interaction. >> >> and I can not understand your this statement "you have to contend with >> forces principally acting perpendicular to the direction of the bias" >> >> > Well, what interactions act along the plane perpendicular to the helix > axis of a duplex DNA or RNA? > > -Justin > > > >> On Tue, Sep 4, 2018 at 10:54 PM, Justin Lemkul wrote: >> >> >>> On 9/4/18 11:44 AM, Rakesh Mishra wrote: >>> >>> Dear Justin, Seriously I want to remove my confusion. I just read your one paper " J.Physical Chemistry B 2010, 114, 1652-60" Where you have studied stability of Alzheimer. I don't want to ask about umbrella sampling used for the calculation of PMF. But , before the calculation of PMF , you have obtained simple dissociation using your pulling protocol of gromacs with constant velocity simulation at three different velocities. I am surprised that you have followed the obvious protocol of minimization the nvt the npt and then 100ns md production. then you took final structure of 100ns and made new box for pulling and followed the same minimisation and npt for short time. After this you did pulling along only one direction (one reaction coordinate) . I am surprised that how such a smooth force/time data you have obtained for all the velocities (0.01,0.001,0.005) . I am asking because for my simple 12bp dsDNA or 22bp siRNA , I also have followed similar protocol and fixed one end (say 5') of first strand and pulling opposite end (5') of second strand along the helical direction of the system. Here, I am getting force/time (in the .xvg ) data which is qualitatively similar behaviour like yours i.e. initially increasing then reach to maximum and then decreasing almost becomes to zero value. But , In mine case during initial time of pulling force is also negative as well large fluctuation of force . But not such a smooth Variation of force/time like your in this paper. In your case, force is increasing like linearly in the initial and reaches the maximum and then start to decrease. There is no problem to clarify the peak of force (maximum force) in your pulling (above mentioned paper). While in our case its very difficult to clarify the peak force due to large fluctuation in value. Can you please tell me something about the reason. Its smoothness is now became headache for my calculation in all the case of pulling. There is no reason to think that your outcome and mine should look >>> anything alike. Pulling apart two proteins that interact in the way the >>> peptides do in a protofibril is much simpler than the intertwined nature >>> of >>> a DNA or RNA duplex. If you pull along the helix axis, you have to >>> contend >>> with forces principally acting perpendicular to the direction of the >>> bias, >>> as well as the fact that the strands have to slide past one another, >>> requiring major distortion of the helix and/or frictional forces due to >>> the >>> individual strands unwinding from one another. >>> >>> -Justin >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Assistant Professor >>> Virginia Tech Department of Biochemistry >>> >>> 303 Engel Hall >>> 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. >>> >>> >> >> > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA
