[gmx-users] Too many LINCS warnings

Dear all, In one of my simulations when I use the command mdrun -v -deffnm nvt I face with this fatal error: Too many LINCS warnings (1056) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but

[gmx-users] How to fix protein went out water?

Dear gmx_users, I am working on simulation of protein in water. 10 ns after the protein went out from water. How to fix this? Can I continue my simulation?  Best regards, Batsaikhan  -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Too many LINCS warnings

Hi, It means your simulation is http://www.gromacs.org/Documentation/Terminology/Blowing_Up Mark On Tue, Jun 17, 2014 at 11:39 AM, h.aliza...@znu.ac.ir wrote: Dear all, In one of my simulations when I use the command mdrun -v -deffnm nvt I face with this fatal error: Too many LINCS

Re: [gmx-users] How to fix protein went out water?

On 6/17/14, 7:56 AM, Batdorj Batsaikhan wrote: Dear gmx_users, I am working on simulation of protein in water. 10 ns after the protein went out from water. How to fix this? Can I continue my simulation? http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin

Re: [gmx-users] peculiar water behavior

Any ideas : 1. why slab is moving despite of position constraints? 2. That too, only with com option of refcoord scaling...with all option slab does not move... Thanks On Sun, Jun 15, 2014 at 7:02 PM, Chetan Mahajan chetanv...@gmail.com wrote: The pics should be seen in the reverse order.

Re: [gmx-users] How to fix protein went out water?

Hi Batsaikhan You should re-do the simulation, perfoming it within a box of water with PBC (you can do this with the editconf) Kind regards Thales 2014-06-17 8:56 GMT-03:00 Batdorj Batsaikhan batsaikhan...@yahoo.com: Dear gmx_users, I am working on simulation of protein in water. 10 ns

Re: [gmx-users] How to fix protein went out water?

On 6/17/14, 10:54 AM, Thales Kronenberger wrote: Hi Batsaikhan You should re-do the simulation, perfoming it within a box of water with PBC (you can do this with the editconf) There is no need to re-do anything. PBC means it is totally irrelevant whether the protein is conveniently

Re: [gmx-users] peculiar water behavior

On 6/17/14, 10:32 AM, Chetan Mahajan wrote: Any ideas : 1. why slab is moving despite of position constraints? Restraints are biasing potentials; they don't prevent movement. Why is it necessary that your slab not move? 2. That too, only with com option of refcoord scaling...with all

Re: [gmx-users] optimize cpu with gpu node for gromacs

Hi, In this case you can't do much, the GPU is simply not fast enough to finish its job before the CPU does. What you can try is: - decrease nstlist - especially if it has been increased by mdrun (hint use GMX_NSTLIST) - try running in mixed GPU+CPU non-bonded mode, e.g. mdrun -ntmpi 2 -gpu_id 00

Re: [gmx-users] Using specbond.dat in pdb2gmx

Dr. Justin Lemkul, Ah I see. I also noticed that in the original specbond.dat, the bond distance specification for the disulfide bonds between 2 CYS's or between 2 CYM's are .2 nm, not .25 nm, so I changed that as well. The only thing I still find a bit unclear is the final columns

Re: [gmx-users] Using specbond.dat in pdb2gmx

On 6/17/14, 1:51 PM, Matthew Stancea wrote: Dr. Justin Lemkul, Ah I see. I also noticed that in the original specbond.dat, the bond distance specification for the disulfide bonds between 2 CYS's or between 2 CYM's are .2 nm, not .25 nm, so I changed that as well. The only thing I still

Re: [gmx-users] Using specbond.dat in pdb2gmx

Or observe that the .rtp entry has names like HB1 and HB2, rather than HB2 and HB3 and use sed (or your text editor) to do the replacement. Mark On Tue, Jun 17, 2014 at 8:09 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/17/14, 1:51 PM, Matthew Stancea wrote: Dr. Justin Lemkul, Ah I

Re: [gmx-users] Using specbond.dat in pdb2gmx

ie. do the replacement on your input coordinate file, not the .rtp! On Tue, Jun 17, 2014 at 10:35 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Or observe that the .rtp entry has names like HB1 and HB2, rather than HB2 and HB3 and use sed (or your text editor) to do the replacement. Mark

Re: [gmx-users] Using specbond.dat in pdb2gmx

Or observe that the .rtp entry has names like HB1 and HB2, rather than HB2 and HB3 and use sed (or your text editor) to do the replacement. ie. do the replacement on your input coordinate file, not the .rtp! Mark Dr. Mark Abraham, My pdb file contains HB1 and HB2 on a beta carbon of a

Re: [gmx-users] Using specbond.dat in pdb2gmx

On 6/17/14, 4:43 PM, Matthew Stancea wrote: Or observe that the .rtp entry has names like HB1 and HB2, rather than HB2 and HB3 and use sed (or your text editor) to do the replacement. ie. do the replacement on your input coordinate file, not the .rtp! Mark Dr. Mark Abraham, My pdb

Re: [gmx-users] peculiar water behavior

Thanks, Justin. That makes it clear. I have one small question: I do not know how does position restraint algorithm work with other things in gromacs, but doesn't it generate a lot of stress due to slab moving from center to near box boundary despite of position restraints, when -com option is

[gmx-users] tunepme does not start

Hi, I try to use mdrun with -tunepme. When I start it at a clusters login node everything works fine. However, when I sent it to a cluster it seems -tunepme gets ignored. mdrun is started and runs the tpr without tuning the number of PME nodes. I attach an example script and a log file. Any

Re: [gmx-users] peculiar water behavior

*Forgot to comment:* *So you are saying: because it is more forgiving, we are observing slab movement in a run with com option for refcoord scaling, and NOT in all option...as such, choosing any one of options com or all for refcoord scaling should not matter simulation results point of view,

Re: [gmx-users] tunepme does not start

On Jun 17, 2014 11:35 PM, Soren Wacker swac...@ucalgary.ca wrote: Hi, I try to use mdrun with -tunepme. When I start it at a clusters login node everything works fine. However, when I sent it to a cluster it seems -tunepme gets ignored. mdrun is started and runs the tpr without tuning the

[gmx-users] CHARMM36 and carbohydrates

Greetings from Taiwan. I am having a bit of trouble setting up a carbohydrate in Gromacs. I have a PDB file that has a glucan chain between a graphene bilayer, but when I run pdb2gmx, it complains of missing atoms. Yes, an oxygen is supposed to be missing because of the 1,4 beta glycosyl

Re: [gmx-users] How to fix protein went out water?

Thank you Justin and Thales. Best regards, Batsaikhan On Tuesday, June 17, 2014 11:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/17/14, 10:54 AM, Thales Kronenberger wrote: Hi Batsaikhan You should re-do the simulation, perfoming it within a box of water with PBC (you can do this