[gmx-users] Jump of drug to other side of lipid bilayer

Dear,I have done a simulation of DMPC lipid bilayer for 50 ns which has 10 drug molecules which were positioned in the water phase in the beginning of simulation. In the first 10 ns of simulation, one of the drug molecules diffuses from water into the other side of lipid bilayer and remains ther

Re: [gmx-users] g_rdf problem

Hi André, Thanks for your paper, so in your opnion the particle C may be kept out of a sphere (like the micelles in your paper, for example)? 2015-07-27 23:06 GMT+08:00 André Farias de Moura : > RDF may behave just like that (slowly growing from 0 to 1 without peaks), > meaning that you have a pa

Re: [gmx-users] Building a Larger Liquid Phase - Truncate 'Vacuum'

On Thu, Jul 30, 2015 at 1:34 PM, Justin Lemkul wrote: > > There are as many DD cells as there are (thread-)MPI processes. These can > be further subdivided into multiple OpenMP threads. What I was talking > about above is the use of only OpenMP, e.g. > > mdrun -ntmpi 1 -nt X > > There is no use

Re: [gmx-users] Building a Larger Liquid Phase - Truncate 'Vacuum'

On 7/29/15 4:25 PM, Elton Carvalho wrote: On Thu, Jun 25, 2015 at 7:39 PM, Justin Lemkul wrote: On 6/25/15 2:46 PM, John Degenstein wrote: I suppose in retrospect that I could simply use a single processor which I think would reduce the number of DD cells and thus prevent this error. Or

[gmx-users] question

Dear gromacs users I want to use LIE to obtain binding free energy for my protein-ligand complex. Can I use 0.181 and 0.5 as alpha and beta coefficients for my system? Are 0.181 and 0.5 appropriate for any kind of protein-ligand complex? Any help will highly appreciated. Best, Atila -- Gromac

Re: [gmx-users] Alchemical free energy calculations - right choice of lambda points? What else might I do wrong?

You're welcome. Please note that improper dihedral term which relates between the dummy atoms and the rest of the molecule needs to be removed ("zeroed") as is explained in Section II. Thanks. Best regards, Asaf Quoting Julian Zachmann : Thanks a lot for your answers!!! I was really sure t

Re: [gmx-users] MD simulations

Please list out the warnings to give you some suggestion On 30 July 2015 at 15:52, hari ram wrote: > Hello Users > > I am using Gromacs for mulecular dyanamic simulation of protein at > different temperature > > i got an error message in energy minimization step > after the following commend >

Re: [gmx-users] Alchemical free energy calculations - right choice of lambda points? What else might I do wrong?

Thanks a lot for your answers!!! I was really sure that the bonded terms to the dummy atoms should be zero so it would have taken me months to find this mistake!! I'm now running the simulations with the lambda points like this: ; 0 1 2 3 4 5

Re: [gmx-users] Settle vs. 3 normal constraints

Dear Mark, thanks a lot for this advice - I've changed my .mdp to lincs-order = 8 and it works just fine! Andreas Am 30.07.2015 um 13:59 schrieb Mark Abraham: Hi, Using "normal" constraint algorithms with triangles of constraints can be tricky with some integrators. Do check out the seve

Re: [gmx-users] Settle vs. 3 normal constraints

Hi, Using "normal" constraint algorithms with triangles of constraints can be tricky with some integrators. Do check out the several manual sections that talk about how these algorithms work, e.g. you may need to increase lincs-order Mark On Wed, Jul 29, 2015 at 5:47 PM Andreas Mecklenfeld < a.m

Re: [gmx-users] Study of sampling of villin headpiece

Hi, I do not think it is sensible to attempt to measure the relative efficiency of two different methods in the absence of evidence that either has sampled approximately ergodically. This is why many approaches to enhance sampling start testing with toy systems like alanine dipeptide. You should c

Re: [gmx-users] a few detailed questions about the topology file format

Hi, On Wed, Jul 29, 2015 at 9:39 PM Eric Smoll wrote: > Hello Gromacs users, > > > As far as I understand, values listed in the top file override any > information pulled from share/gromacs/top. However, ff an atom type (e.g., > "opls_100") serves as a references to information contained in the

Re: [gmx-users] Jumping to other side of box

Hi, You cannot attach items to emails to this list. If you need to share a file, please upload it to one of the many file-sharing services on the web and post the link. However, in this case I think the problem is conceptual. When you are using periodic boundary conditions, you do not have two si

Re: [gmx-users] MD simulations

Hi :) The error is that there are warnings. Well, one warning. A warning from grompp may indicate an inconsistency in the topology (like atom name mismatch), an incompatibility of MDP parameters which grompp corrects automatically (nst*), or a possible pitfall (like too many temperature coupling g

Re: [gmx-users] MD simulations

What is the error displayed when you run grompp? Is it related to the topology mismatch, wrong mdp parameters, domain decomposition error, shake/Lincs error or something else? There are so many possibilities and unless you write the exact error statement issued by grompp it is impossible for anyone

Re: [gmx-users] Alchemical free energy calculations - right choice of lambda points? What else might I do wrong?

Dear Hannes, It means that in many cases dihedral terms do not need to be transformed = not be multiplied by lambda= remain constant. Removing them also reduces the computational efficiency. The alternative is to remove them as is often done ("zero" them). We have shown "not zero" for dihe

Re: [gmx-users] Alchemical free energy calculations - right choice of lambda points? What else might I do wrong?

The argument regards dihedral that was made towards me was about convergence. When you say "_can_ remain constant", what would be the alternative? I would still think "not zero" for bonds and angles. That is really the crucial point here. From: gromacs

[gmx-users] MD simulations

Hello Users I am using Gromacs for mulecular dyanamic simulation of protein at different temperature i got an error message in energy minimization step after the following commend gmx grompp -f minim.mdp -c 2HQA_modified_solv_ions.gro -p topol.top -o em.tpr Fatal error: Too many warnings (

Re: [gmx-users] Alchemical free energy calculations - right choice of lambda points? What else might I do wrong?

Hi, It has been proven both analytically (http://arxiv.org/abs/1310.2112, Section II) and in simulations (http://arxiv.org/abs/1310.2112, Section IV and http://arxiv.org/abs/1501.01514) that the dihedral terms can remain constant in the transformation in relative free energy calculations.