Re: [gmx-users] NVT problem
What do you think the issue is? What the note states there is that it will not print out the following summary section at the end of the log file: R E A L C Y C L E A N D T I M E A C C O U N T I N G On 1 MPI rank, each using 28 OpenMP threads Computing: Num Num CallWall time Giga-Cycles Ranks Threads Count (s) total sum% - Neighbor search1 28 25001 280.413 21148.852 3.8 ... That section is printed out prior to the "Core ..." line in the text above. This has nothing to do with the resulting output from the run, in the coordinate, energy, trajectory files. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Sun, 23 Sep 2018 at 01:56, AKANXA TIWARI wrote: > > hello > i am trying to simulating a protein after run NVT md run i got a not what i > will do. is this not show any problem. > > Back Off! I just backed up nvt.edr to ./#nvt.edr.1# > starting mdrun 'TUBULIN ALPHA CHAIN' > 5 steps,100.0 ps. > step 49900, remaining wall clock time:35 s > Writing final coordinates. > step 5, remaining wall clock time: 0 s > NOTE: Detected invalid cycle counts, probably because threads moved between > CPU cores that do not have synchronized cycle counters. Will not print the > cycle accounting. > >Core t (s) Wall t (s)(%) >Time:70001.93417500.483 400.0 > 4h51:40 > (ns/day)(hour/ns) > Performance:0.494 48.611 > > GROMACS reminds you: "Uh-oh Right Again" (Laurie Anderson) > -- > 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)
On 9/23/18 12:11 PM, AKANXA TIWARI wrote: Hi During simulation of protein after giving grompp ions command i got a note what should i do. NOTE 3 [file ions2.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This note is harmless if the .tpr file is only being used to add ions. Trying to use PME (e.g. by copying an .mdp file that is used for EM or MD) will trigger a fatal error due to the non-zero charge of the system. So .mdp files specifying plain cutoffs are necessary for adding ions, but should not be used for anything else. -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] (no subject)
In your .mdp file ...in cut-off you mention PME... On Sun, Sep 23, 2018, 9:42 PM AKANXA TIWARI wrote: > Hi > During simulation of protein after giving grompp ions command i got a note > what should i do. > NOTE 3 [file ions2.mdp]: > You are using a plain Coulomb cut-off, which might produce artifacts. > You might want to consider using PME electrostatics. > -- > 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] (no subject)
Hi During simulation of protein after giving grompp ions command i got a note what should i do. NOTE 3 [file ions2.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. -- 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] A question about Protein-Protein interaction with Gromacs
In many cellular signaling pathways in cancer cells, the expression of many genes rises. One result of this excessive expression is cellular traffic and unwanted interactions between proteins. Therefore, it is important to examine the interactions and identify the amino acids involved in the interactions. There are several ways to examine the interactions such as string and using molecular docking. Today, many Docking softwares are active on web servers like Haddock, cluspro, zdock, etc; but, to my mind, examining the interaction between proteins using docking, based on several different reasons, has low credibility that makes the results of these softwares unreliable. That's why I decided to examine it with a better method. For this purpose, I used the molecular dynamics simulation method to locate the molecules under dynamic conditions to make it easier to study the interactions between amino acids (fluctuations, pi pi, hydrogen, and electrostatic bonds). The procedure is as follows: 1- Two proteins were received from the RCSB site. 2- Two proteins were placed at 6-angstrom distance using the Discover Studio software. First question is: Please suggest another way to do this procedure via software (considering the desired position) (according to the available data in the literature) (i.e. the hot spot amino acids) (involved in the interaction) to place two proteins of appropriate position in front of each other? And the next question is whether the 6-angstrom gap between two proteins is sufficient? 3- From the topology building process with pdb2gmx to indexing like the rest of the Justin Lamquell site tutorials were done (Multiple chain tutorial). But the problem is choosing the size of the box to reduce the simulation time. Please suggest a way to find the appropriate box size for two proteins in a box. 4- In order to force the interaction of two proteins, the Pull code tutorial was used. It should be noted that a protein was used to capture RMSD; i.e. the protein stabilization was screened. Please suggest a more precise way to analyze, develop, and validate this method. -- 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.
