Re: [gmx-users] Inexpected rmsd
Dear Emran Heshmati, I can not see any graph? Did you attach it. Please verify. Thank you On Fri, Mar 27, 2020 at 6:21 PM Emran Heshmati wrote: > I am working on a protein consisting 2 chains. After performing regular MD > simulation and analysis the outputs, I got unexpecter rmsd, as shown in > arttached graph. What is the problem? > -- > 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] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation
Dear Amit, Yes, you need to correct the atom number in the "zn.itp" file in your case. >From your co-ordinate file, it is clear that in order to restrain Zn atom you need to put restraint potential on atom number corresponding to Zn atom which is 4265 in your case instead of 2220. I think this should fix the problem in your case. Try it and let me know if the problem persists. Thank you. On Tue, Oct 22, 2019 at 1:12 PM Amit Jaiswal wrote: > Dear Jorden, > > Thanks for your reply. As you have suggested, i found there is a mismatch > of the atom number in the zn.itp file and the .gro file. I have included > few residues of .gro file for your convenience. > > What i understand is that I have to rename the zn.itp file with residue > no. 4265 and not 2220. Please correct me if I am wrong. > > And also you suggested me to "minimize the system very carefully". What do > you mean by this? Should i use lesser minimisation steps ? > > Thanks for your time and efforts. > > With kind regards, > Amit > > 391THR HG22 4260 4.897 5.356 3.136 > 391THR HG23 4261 4.889 5.247 2.993 > 391THR C 4262 4.600 5.071 3.244 > 391THR OT1 4263 4.599 5.012 3.355 > 391THR OT2 4264 4.496 5.082 3.173 > 392ZN ZN 4265 7.278 6.612 5.838 > 393NAD PA 4266 6.217 7.359 2.802 > 393NAD O1A 4267 6.090 7.410 2.863 > 393NAD O2A 4268 6.337 7.451 2.808 > 393NAD O5B 4269 6.185 7.331 2.647 > 393NAD C5B 4270 6.082 7.233 2.620 > > > > 19.10.2019, 21:53, "Jorden Cabal" : > > Dear Amit, > Your files look correct to me. If "2220" atom in your coordinate file is > the "Zn" atom, it should not be displaced because, from your mdp file and > topology setting you have restrained all the heavy atoms of Protein, Nad > and Zn. I don't understand why it is happening. Even the restraining force > you are taking is good enough. > I suggest you to check if the atom number 2220 in the co-ordinate file > (.gro file) is Zn atom or not? If it is not then you have wrongly selected > atom number for restraining. Also, if you are following the standard > tutorial for energy minimization which do not restrain any atom, I suggest > you to check the position of Zn atom in structure you get after energy > minimization. If the location of Zn ion is changed during the EM, then you > will need to minimize the system very carefully. > Hope this will fix your issue. > Thank you > -- > Gromacs Users mailing list > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > 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] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation
Dear Amit, Your files look correct to me. If "2220" atom in your coordinate file is the "Zn" atom, it should not be displaced because, from your mdp file and topology setting you have restrained all the heavy atoms of Protein, Nad and Zn. I don't understand why it is happening. Even the restraining force you are taking is good enough. I suggest you to check if the atom number 2220 in the co-ordinate file (.gro file) is Zn atom or not? If it is not then you have wrongly selected atom number for restraining. Also, if you are following the standard tutorial for energy minimization which do not restrain any atom, I suggest you to check the position of Zn atom in structure you get after energy minimization. If the location of Zn ion is changed during the EM, then you will need to minimize the system very carefully. Hope this will fix your issue. Thank you -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation
Dear Amit, During equilibration you add positional restraint for protein, notice that you have added positional restraint for Zn ion, nad and protein. It should not happen if you have taken the default values while generating the positional restraints in gromacs. However I would like to look to your "nvt.mdp", "posre_zn.itp" and "posre_nad.itp" files, in order to comment on it. Thank you On Sat, Oct 12, 2019 at 1:50 PM Amit Jaiswal wrote: > Dear Jorden, > > Many thanks for your suggestions. I solved the index file problem as I > created two groups namely Protein_Zn_NAD and the other being Na_Water. But > when i ran NVT equilibration, the Zn ion again got displaced far away from > its original position. I cannot figure out how can i constrain the Zn ion? > I guess something is wrong in the topology file. I have included the last > few lines of my topology file. Please have a look whenever you are free and > correct me if something is mistakenly wrong. Thanks for your time and help. > > > *; Include Position restraint file* > *#ifdef POSRES* > *#include "posre.itp"* > *#endif* > > *; Include Position restraint file* > *#ifdef POSRES* > *#include "posre_zn.itp"* > *#endif* > > *; Include ligand topology* > *#include "nad.itp"* > > *; Ligand position restraints* > *#ifdef POSRES_LIG* > *#include "posre_nad.itp"* > *#endif* > > *; Include water topology* > *#include "./charmm36-mar2019.ff/tip3p.itp"* > > *#ifdef POSRES_WATER* > *; Position restraint for each water oxygen* > *[ position_restraints ]* > *; i funct fcx fcy fcz* > *1 1 1000 1000 1000* > *#endif* > > *; Include topology for ions* > *#include "./charmm36-mar2019.ff/ions.itp"* > > > *[ system ]* > *; Name* > *Protein in water* > > *[ molecules ]* > *; Compound #mols* > *Protein_chain_A 1* > *ZN 1* > *NAD 1* > *SOL 12908* > *NA 4* > > With kind regards, > Amit > > 11.10.2019, 18:10, "Jorden Cabal" : > > Dear Amit, > Please check if the Zn ion is included in both the groups declared for > temperature coupling. If you notice that it is is included, you can simply > create a group of all the atoms which is not in "Protein_NAD" group. You > can do this by using "!group_number" as far as I remember. Then try this, > it should work. Please mail if the problem persists. > Thank you and all the best. > -- > 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] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation
Dear Amit, Please check if the Zn ion is included in both the groups declared for temperature coupling. If you notice that it is is included, you can simply create a group of all the atoms which is not in "Protein_NAD" group. You can do this by using "!group_number" as far as I remember. Then try this, it should work. Please mail if the problem persists. Thank you and all the best. -- 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] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation
Hi Amit, The metal ion needs to be treated very very carefully so as to maintain their co-ordination state with the nearby atoms of protein. To do this, one needs to generate the parameter separately for the complex formed by the metal ion with the protein residues because due to presence of metal ion in the vicinity, the residues nearby will have different parameters than other proteins especially the charge distribution. One method of incorporating this model is to model the metal ion as a dummy-particle metal ion complex model where the dummy particles carry some partial charge and the whole complex represent the co-ordination state of that particular atom. I would suggest you to go through this paper https://pubs.acs.org/doi/pdf/10.1021/jp501737x In case, you do not want to go in that much detailed modeling of metal ion for your system, which I think is very important to study metalloproteins, another very simple method of solving the problem you are facing is to treat metal ions as single sphere as you are treating in your system. To avoid its displacement from its location, you need to apply some distance restraints which is very easy to apply in Gromacs. You can create the distance restraint using "*genrestr*" command. Please note that applying any kind of restraint will definitely add some bias to your simulation. Thank you On Thu, Oct 10, 2019 at 1:05 PM Amit Jaiswal wrote: > Hello Everyone, > > Would you please let me know what should we do when the zinc ion gets > displaced during simulation of a Protein-Zn-Ligand complex? What are the > possible options one can perform under such conditions? If possible, please > mention the steps needed to be performed briefly as i am new to GROMACS. > Your suggestions will help me a lot and thanks in advance. > > With kind regards, > Amit > -- > 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] Extracting trajectory
Hi Anupama, I understand your question. But I wonder why do you want all the explicit water molecules within 5 Angstrom of your protein surface? That would be meaningless until and unless you are intending to find the conserved water molecules near the surface of protein. I don't understand your purpose, but trjcat can not dynamically change the selection automatically at each frame so directly it is not possible. Instead you can get the trajectory in appropriate format by using the "mindist" command which is used for calculating the contacts between two groups. Please see the options available with this command, you will find "-ox" option which will give you the required trajectory. For example let's say, original trajectory=traj.xtc tpr=run.tpr Index=index.ndx (group 1 for protein and 13 for sol) the the command should look like this: *gmx mindist -f traj.xtc -s run.tpr -n index.ndx -o output.out -n output.xvg -ox required_traj.xtc -d 0.5 -group* After being asked you will have to select appropriate group like 1 and 13 for protein and sol from the index file. The output file required_traj.xtc will contain all the water molecules within 5 Angstrom of protein. *Important Notes: * 1: Since there are large number of water molecules in the system, the calculation time will be very very high. I have not estimated so can not comment on this but I am sure that it will take a long. 2: You will not be able to visualize the .xtc file directly using visualization package like vmd as they require corresponding .gro file. But in this case the index of the water molecules will change per frame so its not possible. Instead you can directly write in the gro/pdb formats. *Although, I do not understand the purpose of your question, I still suggest you to make intelligent choice of identifying water molecules near to some interesting cavity instead of whole surface. This will save your computational time. You can see the following paper for your reference.* https://www.tandfonline.com/doi/abs/10.1080/1062936X.2018.1537301?journalCode=gsar20 I hope this will solve your problem. Thank you Jorden On Wed, Oct 2, 2019 at 10:32 PM anupama sharma wrote: > Dear users, > I want to extract the trajectory of water molecules near the protein > surface within 5 angstorm region. I was able to do that in using gmx select > and gmx trjcat, but it is for only one time frame and than the water > molecules diffuses away for the next time frame. I want to extract the > trajectory of only those water molecules that are near protein surface > within 5 angstorm region for each individual time frame so that i can get > the complete trajectory of water molecules that are near the protein > surface excluding the water molecules that diffuses away in each next > frame.. > I will be thankful for help. > > > > > Thanks and regards, > Anupama > -- > 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] "comm-mode = Angular" gives error
Hi Justin, Thank you Justin for letting me know. I will definitely consider increasing the simulation box. Although, I was wondering that what would happen if I take comm-mode="Angular" and comm-grps= "molecule_AB !molecule_AB". This setting gives a warning which was ignored using -maxwarn option. After running 10 ns of simulation, the system seems to be stable and very less fluctuations are observed upon visualization compared to when I use comm-mode="Linear". or nothing. What would you suggest? Should I proceed with the first setting? Thank you in advance. On Tue, Aug 20, 2019 at 9:25 PM Justin Lemkul wrote: > > > On 8/20/19 5:21 AM, Jorden Cabal wrote: > > Hi Justin, > > Thank you for your response. In my case the cost of increasing simulation > > box is very large. I have already tried it by keeping distance between > the > > periodic images of the macromolecule up to 50 Angstrom. Could you suggest > > me any other option to do this. In Gromacs, rotation around pivot can be > > enforced, is it possible to use this method somehow to counter the > > rotation? Even if its possible, how and to which extent do you think it > > will add biasness to the independent behavior of the macromolecule. Any > > suggestions, comments in this regard will help me. > > You can apply biasing potentials to avoid rotation, but then you're > seriously perturbing the dynamics in a way that might completely bias > your results (I don't have nearly enough context to say for sure, so > I'll be a bit circumspect). If you have a large molecule that rotates, > you need a large box that reflects that intrinsic symmetry. It's the > same reason you can't build a long, rectangular box around a DNA duplex. > If it rotations orthogonal to the longest axis, it sees it's image and > the forces are invalid. > > There are no real "tricks" here. If you have a big molecule, you need a > suitably large box. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Error in calculating center of mass using distance command
Hi Sumedha, I think you are using the default value of -len (i.e Mean distance for histogramming) in the command which is 0.1. If you data points contains distance values which has larger mean than this, histogramming for those values will not be calculated. For conformation, you can check the output file, you will see that it ends 0.2. I hope this might help you. Thanks On Wed, Aug 21, 2019 at 10:54 PM Justin Lemkul wrote: > > > On 8/21/19 9:52 AM, Sumedha Bhosale wrote: > > Hello, > > > > I am trying to calculate the center of mass of residues 513-515 and > 588-590 > > of chain A and chain B using distance command. I want output in histogram > > format. But it seems that distance command is a calculating the distance > of > > my first group and itself. It's not taking the second group. I am getting > > all values as zero in histogram plot. > > I have made index files for two separate groups of chain A and chain B. I > > am using the command - com of group 34 plus com of group 35. > > Please provide the exact command you gave, directly copied and pasted > from the terminal. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] "comm-mode = Angular" gives error
Hi Justin, Thank you for your response. In my case the cost of increasing simulation box is very large. I have already tried it by keeping distance between the periodic images of the macromolecule up to 50 Angstrom. Could you suggest me any other option to do this. In Gromacs, rotation around pivot can be enforced, is it possible to use this method somehow to counter the rotation? Even if its possible, how and to which extent do you think it will add biasness to the independent behavior of the macromolecule. Any suggestions, comments in this regard will help me. Thank you On Mon, Aug 19, 2019 at 8:00 PM Justin Lemkul wrote: > > > On 8/19/19 12:39 AM, Jorden Cabal wrote: > > Dear Users, > > I am trying to perform simulation of a very large and complex system and > > which requires me to make the simulation box rectangular cube instead > (box > > dimension 24.5 nm * 12.5 nm * 12.3 nm) of perfect cuboid in order to > > minimize the number of atoms present in the system. > > > > I am facing the problem of interaction between periodic images due to > > rotational movement of the macro molecule. I have tried lowering the > > *nstcomm* (frequency of removal of center of mass velocity) to 10 and it > > seems it might work but the speed become very slow because it also > requires > > *nstcalcenergy* to 10. > > > > When I use *comm-mode="Angular"* with *comm-grps="system" *it says "*too > > many warnings*" and the warning is > > *"Removing the rotation around the center of mass in a periodic system, > > this can lead to artifacts. Only use this on a single (cluster of) > > molecules. This cluster should not cross periodic boundaries*" > > > > *"Although this problem can be ignored using -maxwarn option in the > grompp > > command. I want to know that if that is the correct thing to do?" * > > > > *Instead, *I have also tried to work this out by changing the* comm-grps= > > "Protein" *but then it throws two warnings first being the same as > > mentioned above and the second warning says "*Some atoms are not part of > > any center of mass motion removal group. This may lead to artifacts. In > > most cases one should use one group for the whole system*" > > > > Again this can be ignored using -maxwarn option but is that right to do? > > Please suggest me regarding this. > > This is not the purpose of comm-mode/comm-grps, which account for net > COM motion as a function of other errors in the simulation (Google the > "flying ice cube effect"). You can't prevent your molecules from > rotating in any physically realistic way. The simulation box needs to be > larger to avoid these interactions, and comm-mode/comm-grps is not the > way to get around it. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] (no subject)
I think the answer is not so straightforward. It depends upon a lot of things, but I would say that the parameters derived using QM is better. If you do not have any other options you can still use PRODRG server but even in that case, I find many people using the docked (or bound) conformation of the Ligand molecule to generate the initial parameters, which in my view should not be done. One should generate the parameters using the molecule in its minimum energy conformation instead of bound conformation. I would also suggest you to look at the RED server. Please follow this link https://upjv.q4md-forcefieldtools.org/RED/ Thank you On Mon, Aug 19, 2019 at 3:00 PM Priyanka Singh wrote: > Hii > I am new to simulations. I want to ask is it ok to use ligand topology > build using PRODRG server if using amber force field for RNA-ligand > simulation. what precautions one should take ends of the RNA molecule. > -- > 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] "comm-mode = Angular" gives error
Dear Users, I am trying to perform simulation of a very large and complex system and which requires me to make the simulation box rectangular cube instead (box dimension 24.5 nm * 12.5 nm * 12.3 nm) of perfect cuboid in order to minimize the number of atoms present in the system. I am facing the problem of interaction between periodic images due to rotational movement of the macro molecule. I have tried lowering the *nstcomm* (frequency of removal of center of mass velocity) to 10 and it seems it might work but the speed become very slow because it also requires *nstcalcenergy* to 10. When I use *comm-mode="Angular"* with *comm-grps="system" *it says "*too many warnings*" and the warning is *"Removing the rotation around the center of mass in a periodic system, this can lead to artifacts. Only use this on a single (cluster of) molecules. This cluster should not cross periodic boundaries*" *"Although this problem can be ignored using -maxwarn option in the grompp command. I want to know that if that is the correct thing to do?" * *Instead, *I have also tried to work this out by changing the* comm-grps= "Protein" *but then it throws two warnings first being the same as mentioned above and the second warning says "*Some atoms are not part of any center of mass motion removal group. This may lead to artifacts. In most cases one should use one group for the whole system*" Again this can be ignored using -maxwarn option but is that right to do? Please suggest me regarding this. Thank you -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
