Re: [gmx-users] gmx wham (again)

An otherwise perfectly well-behaved setup is doing something catastrophic. The pull code is: ; Pull code pull = yes pull-coord1-type = umbrella pull_ngroups= 2 pull_ncoords= 1 pull_group1_name= K pull_group2_name= CNT

Re: [gmx-users] gmx wham (again)

... and everything is segfaulting, though worked perfectly fine until the 'cylinder' thing. On Wed, Apr 18, 2018 at 3:45 PM, Alex wrote: > Which then would be = 0 0 1, correct? This though will have to coexist > with pull_coord1_rate= 0.0 > > Is that reasonable? > >

Re: [gmx-users] gmx wham (again)

Which then would be = 0 0 1, correct? This though will have to coexist with pull_coord1_rate= 0.0 Is that reasonable? Thanks, Alex On Wed, Apr 18, 2018 at 2:11 PM, Justin Lemkul wrote: > > > On 4/18/18 4:08 PM, Alex wrote: > >> In addition, we seem to have a

Re: [gmx-users] GPU Command

I would try to tune your launch with a ~100 ps run, testing several different options for optimal performance (it can really save some time). Performance will be very dependent on your CPUs in the setup that you mentioned, so I would recommend installing GROMACS 2018 to offload PME to the GPU,

Re: [gmx-users] gmx wham (again)

On 4/18/18 4:08 PM, Alex wrote: In addition, we seem to have a different problem: Cylinder geometry requires the use of pull-coord1-vec, not pull-coord1-dim. -Justin --- Program: gmx grompp, version 2018 Source file:

Re: [gmx-users] gmx wham (again)

In addition, we seem to have a different problem: --- Program: gmx grompp, version 2018 Source file: src/gromacs/gmxpreprocess/readpull.cpp (line 234) Fatal error: With pull geometry cylinder the pull vector can not be 0,0,0 On Wed, Apr

Re: [gmx-users] gmx wham (again)

This is the exact situation that the "cylinder" pull geometry is designed to model. I suggest going that route rather than ad hoc restraints, which will influence the PMF and should be otherwise accounted for. -Justin Hi Justin, Thanks. To make sure things are more or less reasonable, I'd

Re: [gmx-users] Gromacs 2018 and 2018.1 bug? Atoms/molecules in freezegrps keep moving

Hi Mark, Thanks for responding. I have filed an issue on redmine.gromacs.org Best regards, Tai -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: 18 April 2018 15:28 To:

Re: [gmx-users] Gromacs 2018 and 2018.1 bug? Atoms/molecules in freezegrps keep moving

Hi, As far as I know nothing relevant should have changed, but if you would like us to investigate further, please open an issue at https://redmine.gromacs.org/ and attach the .tpr files that used to work and now do not. Your 2018.x .log files might also be helpful. Thanks! Mark On Wed, Apr

[gmx-users] Gromacs 2018 and 2018.1 bug? Atoms/molecules in freezegrps keep moving

Dear all, I am using gromacs version 2018 and 2018.1. However I figured that when I freeze a group of atoms/molecules (water) using freezegrps (NVT ensemble), the frozen atoms kept moving and the simulation terminated due to too many LINCS warnings. This problem never happened before for

Re: [gmx-users] trjconv ndec not working

On 4/18/18 8:57 AM, Dawid das wrote: The quick and dirty solution is that I write gro and g96 and copy coordinates from the latter to the former, but I'd rather have more elaborate solution. .gro files are fixed-format, and in current GROMACS versions it is not possible to write more

Re: [gmx-users] Regarding Coulomb-14 Energy

On 4/18/18 5:49 AM, za...@tezu.ernet.in wrote: Dear Mark Thank you for the kind response. H with +0.418 charge and N with -0.845 charge is contributing towards coulomb 14 interaction. So what is the amount of interaction between one single H and N (3 bonds apart)? Kindly correct me if I am

Re: [gmx-users] gmx wham (again)

On 4/18/18 3:17 AM, Alex wrote: I suppose this question is mostly for Justin... Let me remind what I am dealing with and ask if my idea is correct. I have a rectangular membrane in XY with a pore at (X/2, Y/2) in water and want to get the Gibbs free energy curve for an ion. For this, I

Re: [gmx-users] trjconv ndec not working

The quick and dirty solution is that I write gro and g96 and copy coordinates from the latter to the former, but I'd rather have more elaborate solution. 2018-04-18 14:53 GMT+02:00 Dawid das : > Dear All, > > I have similar issue. I have created xtc file with precision of

Re: [gmx-users] trjconv ndec not working

Dear All, I have similar issue. I have created xtc file with precision of 1.0e-6 nm and I want my gro file to have the same precision, and I get this at the end of trjconv Reading frame 0 time3.000 Precision of npt-md-prod.xtc is 1e-06 (nm) Setting output precision to 1e-06 (nm) Last

Re: [gmx-users] Regarding Coulomb-14 Energy

Hi, On Wed, Apr 18, 2018 at 10:50 AM wrote: > >> Dear Mark > >> Thank you for the kind response. > >> H with +0.418 charge and N with -0.845 charge is contributing towards > coulomb 14 interaction. So what is the amount of interaction between > one > >> single H and N (3

Re: [gmx-users] Error in gmx trjcat

> Hi, > > Probably something like an upgrade of the OS or compiler version changed > the libraries that it linked to at run time and somehow the checks to > prevent such problems didn't work. If you would recompile GROMACS on that > machine, it would likely be fine. Hey Mark, Thanks for the

[gmx-users] Regarding Coulomb-14 Energy

>> Dear Mark >> Thank you for the kind response. >> H with +0.418 charge and N with -0.845 charge is contributing towards coulomb 14 interaction. So what is the amount of interaction between one >> single H and N (3 bonds apart)? Kindly correct me if I am wrong. Thank you Justin for your kind

Re: [gmx-users] Length of a constrained bond

Hi, >From the topology Mark On Tue, Apr 17, 2018, 22:05 Eric Smoll wrote: > Hello Gromacs Users, > > When setting "constraints=h-bonds" in an mdp file, what sets the > constrained bond length? Is it the equilibrium bond length in the topology, > the bond length deduced

Re: [gmx-users] Error in gmx trjcat

Hi, Probably something like an upgrade of the OS or compiler version changed the libraries that it linked to at run time and somehow the checks to prevent such problems didn't work. If you would recompile GROMACS on that machine, it would likely be fine. Mark On Wed, Apr 18, 2018, 05:37 Syed

[gmx-users] GPU Command

On Thu, Apr 12, 2018 at 4:47 PM wrote: > >> Dear Gromacs Users >> >> We have a GPU Server (Intel(R) Xeon(R) CPU E5-2609 v4 @ 1.70GHz, 16 >> cores) >> with 2 NVIDIA Tesla P100 (12GB) cards. >> >> What should be my final mdrun command so that it should utilize both the >>

[gmx-users] gmx wham (again)

I suppose this question is mostly for Justin... Let me remind what I am dealing with and ask if my idea is correct. I have a rectangular membrane in XY with a pore at (X/2, Y/2) in water and want to get the Gibbs free energy curve for an ion. For this, I have a bunch of starting