Re: [gmx-users] supervised MD in Gromacs?

Hi: Here it is: Supervised Molecular Dynamics (SuMD) as a Helpful Tool To Depict GPCR–Ligand Recognition Pathway in a Nanosecond Time Scale http://pubs.acs.org/doi/abs/10.1021/ci400766b In this work, the author captured the ligand binding process in 60 ns. Here is another one: Binding

Re: [gmx-users] supervised MD in Gromacs?

That's a little bit strange. As in paper: Binding pathway of histamine to the hH4R, observed by unconstrained molecular dynamics http://www.sciencedirect.com/science/article/pii/S0960894X15000645 The author claimed that all the simulation was done in Gromacs I contacted them several times,

[gmx-users] supervised MD in Gromacs?

Dear: I noticed that several paper successfully captured the process of ligand binding to a protein deep pocket in tens of ns time scale MD simulations without any biased. It is a really impressive an useful method. I am just wondering can we do this in Gromacs? Thanks a lot Albert --

Re: [gmx-users] supervised MD in Gromacs?

The only thing you need is to arrange the existing gromacs utilities into a script. Python, Perl, Bash languages do this very well. P.S. It is not very honest of the algorithm authors to call it *unconstrained* while they simply disregard motions that they do not like. On Tue, Dec 8, 2015 at

Re: [gmx-users] supervised MD in Gromacs?

> It is not very honest of the algorithm authors to call it *unconstrained* while they simply disregard motions that they do not like. Thought exactly the same thing :) /J On Tue, Dec 8, 2015 at 1:45 PM, Vitaly V. Chaban wrote: > The only thing you need is to arrange the

Re: [gmx-users] supervised MD in Gromacs?

Dear Albert, You'll have to provide more information. As it is, I doubt anyone understands what you're referring to. What method is it? Where is it presented? Etc. Best regards, João On Tue, Dec 8, 2015 at 11:01 AM, Albert wrote: > Dear: > > I noticed that several paper

Re: [gmx-users] using SPC water with Charmm FF

On 12/8/15 8:32 AM, Smith, Micholas D. wrote: I would mildly disagree with Justin on this one. Although Charmm should ideally be used with TIP3P (as Justin noted being one of the force-field developers and all), there have been a number of papers that show that SPC/E is not entirely incorrect

Re: [gmx-users] supervised MD in Gromacs?

On 12/8/15 8:29 AM, Albert wrote: That's a little bit strange. As in paper: Binding pathway of histamine to the hH4R, observed by unconstrained molecular dynamics http://www.sciencedirect.com/science/article/pii/S0960894X15000645 The author claimed that all the simulation was done in

Re: [gmx-users] using SPC water with Charmm FF

I agree, Justin, that the gold-standard would be to compare SPC derived values to TIP3P in a very systematic way; however, it isn't just pure-water, small peptides, and disordered peptides that show that SPC can be used with Charmm. Indeed a recent binding study (Effects of water models on

Re: [gmx-users] Writing checkpoint

On 12/8/15 10:17 AM, masoud keramati wrote: hi to all in the mdrun log file i see "Writing checkpoint, step 47840 at Tue Dec 8 18:42:52 2015". what means of this Writing checkpoint? mdrun is writing a checkpoint file. You can use it to extend the run, restart after a power outage, etc.

Re: [gmx-users] supervised MD in Gromacs?

Dear Joao: thanks again for such kind comments. I know Plumed can perform similar work probably if we define the distance between the ligand and binding pocket as the CV. However, I am not so sure whether such kind of metadynamic simulation will lead to a nice ligand binding mode in the end,

Re: [gmx-users] supervised MD in Gromacs?

Dear Albert, Unfortunately, the methods section of some papers does not reflect every detail of what was done to achieve the results. In the particular case of computational papers, this means the use of scripting (or even hacking) to assist a more wide-spread code (like GROMACS). That being

Re: [gmx-users] supervised MD in Gromacs?

Thanks for the comments. In this case, it is probably meaningless to compare the kinetic of two ligand based on the time that ligand jump from bulk water into the binding pocket.Neither could one be sure that the final pose is close to the crystal structure. regards Albert On

[gmx-users] gromacs openmpi error

Hi everyone, I want to install gromacs in the GPU, I have installed fftw-3.3.tar.gz openmpi-1.6.5cmake-3.0 gromacs-4.6.5.tar.gz if I use several nodes, it appears error MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking

Re: [gmx-users] using SPC water with Charmm FF

I would mildly disagree with Justin on this one. Although Charmm should ideally be used with TIP3P (as Justin noted being one of the force-field developers and all), there have been a number of papers that show that SPC/E is not entirely incorrect (see below). What you would need to do is see

Re: [gmx-users] supervised MD in Gromacs?

In addition to what Justin said, please notice that the reference by Wittmann et al does not use SuMD. From what I read it uses standard MD simulations. The other reference, where SuMD is actually presented, gives all necessary information to produce your own version of it, since the authors are

Re: [gmx-users] supervised MD in Gromacs?

Albert, we need to get some things straight: 1) Please notice that your affirmation about failing to report a method in a paper published through a peer-reviwed journal is quite serious, and can have consequences. 2) The authors are entitled to comercialize their intellectual property. It's not

Re: [gmx-users] supervised MD in Gromacs?

Hi Albert, A simple script to run: 1) a short simulation 2) g_dist/gmx distance 3) g_analyze/gmx analyze 4) decide to continue the simulation from the final coordinates or restart the simulation from the initial coordinates should do the trick I think to reproduce the SuMD method given in

[gmx-users] Writing checkpoint

hi to all in the mdrun log file i see "Writing checkpoint, step 47840 at Tue Dec 8 18:42:52 2015". what means of this Writing checkpoint? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?

Re: [gmx-users] Writing checkpoint

On 12/8/15 11:36 AM, masoud keramati wrote: can i run gromacs in parallel using two different computers? I think you should spend some time reading the manual, website, mailing list archive, and published GROMACS papers. -Justin On 12/8/15, Justin Lemkul wrote:

Re: [gmx-users] Writing checkpoint

can i run gromacs in parallel using two different computers? On 12/8/15, Justin Lemkul wrote: > > > On 12/8/15 10:17 AM, masoud keramati wrote: >> hi to all >> >> in the mdrun log file i see "Writing checkpoint, step 47840 at Tue Dec >> 8 18:42:52 2015". >> what means of

Re: [gmx-users] Writing checkpoint

ok tnx for ur respond On 12/8/15, Justin Lemkul wrote: > > > On 12/8/15 11:36 AM, masoud keramati wrote: >> can i run gromacs in parallel using two different computers? >> > > I think you should spend some time reading the manual, website, mailing list > > archive, and

Re: [gmx-users] grid cell out of range

Hi, First obvious thing: v4.6.1 is severely outdated, so is the compiler used, gcc 4.4. Does 4.6.7 compiled with something more recent reproduce the issue? Cheers, -- Szilárd On Mon, Dec 7, 2015 at 6:14 PM, Fabricio Cannini wrote: > Hello > > I have a user complaining of

Re: [gmx-users] Distance between atom A and the nearest image of atom B

Hello, Michael, This is covered in the file src/gromacs/gmxlib/pbc.c in the gromacs distribution. On Sun, Dec 6, 2015 at 7:16 AM, Michael Cristòfol Clough < michaelcristo...@gmail.com> wrote: > Hello everyone, > > I'm writing a little program and I want to calculate the distance between > atom

Re: [gmx-users] Fwd: Help with Gromacs 5.1 mdp options for CHARMM27 force field

Hi Justin, Thanks for the reply. I have few more doubts regarding the mdp settings and gmx tools related analysis. 1) What are the optimal values of tau_t and tau_p for CHARMM36. I see in your tutorial that it is 0.1 0.1 for tau_t and 2.0 for tau_p. The CHARMM-GUI generated mdp settings had