[gmx-users] Settle vs. 3 normal constraints

Dear GROMACS users, I want to calculate the solvation free energy of a rigid water molecule, e.g. TIP4P-Ew. To do this, I define one solute molecule which I refer to as couple-moltype in the .mdp-file (SOL). The solvens molecules are exactly the same, just named differently for distinction

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

Dear Gromacs-Users, I calculate relative binding energies using free energy perturbation (FEP) and mbar. I have the binding data for 4 receptors and two ligands which are almost identical. The only difference is the change from a methyl group to a hydrogen. I alchemically convert a methyl group

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

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 share/gromacs/top directory, is it necessary to include a value for

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

On Thu, Jun 25, 2015 at 7:39 PM, Justin Lemkul jalem...@vt.edu 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 just use OpenMP

[gmx-users] Jumping to other side of box

Dear Users, I have done a simulation of DMPC lipid bilayer which has 10 drug molecules in the water phase for 50 ns. In the first 10 ns of simulation, one of the drug molecules diffuses from water into the other side of lipid bilayer and remains there. I applied (trjconv –pbc mol), (trjconv

[gmx-users] Study of sampling of villin headpiece

Dear all, Due to the computational facilities that I can use I am running 5000 ps simulations with the villin headpiece system and I am trying to compare the sampling efficiency of two different methods. Since for this short simulations, I am not able to observe the folding phenomena, what would

Re: [gmx-users] Measuring Bilayer thickness with gmx distance in CGMD simulations

Hi Carlos, this *should* work. In our lab we usually look at density profiles along the z-axis; that way you get a sense of distribution. Additionally, depending on the size of your bilayer, you will need to correct for undulations (non-trivial). Peter Kroon On 28/07/15 20:54, Carlos Navarro

Re: [gmx-users] on MD simulation of ATP hydrolysis driven protein conformational change

Dear Brett: The answer to your questions is yes. In our lab, we use MD simulations to study and identify the ATP-hydrolysis induced conformational changes in several ABC transporters (both exporters and importers). You can check our papers if you are interested: - Insights into the

[gmx-users] Fwd: Question about editconf -noc flag

Hi all, I have made an oil slab (energy minimized, equilibrated nvt and npt), some of the oil molecules are at the other end (periodicity). https://drive.google.com/open?id=0B0YMTXH1gmQsYmdvQ3huYWtDaGs then I decided to increase the box size in z direction a bit to make enough room for protein,

Re: [gmx-users] Issues using tabulated potentials for coarse-grained simulation

Many thanks Brian ! On Tue, Jul 28, 2015 at 12:50 AM, Brian Yoo brian.s.yoo...@nd.edu wrote: Hi Tamrisa, Sorry for the slow response. Was a bit busy this weekend. I'm guessing you are using Bhargava and Klein's model? I made a mistake in setting the number of exclusions to 3 rather than 2

Re: [gmx-users] performance of e5 2630 CPU with gtx-titan GPU

Hi Netaly, in this study http://arxiv.org/abs/1507.00898 are GROMACS performance evaluations for many CPU/GPU combinations. Although your combination is not among them, you could try to estimate its performance from similar setups. There is for example an E5-1620 CPU with a TITAN GPU. Although

Re: [gmx-users] performance of e5 2630 CPU with gtx-titan GPU

thanks a lot for your answer. I will definitely take a look on this study. Regards, Netaly On Wed, Jul 29, 2015 at 11:22 AM, Kutzner, Carsten ckut...@gwdg.de wrote: Hi Netaly, in this study http://arxiv.org/abs/1507.00898 are GROMACS performance evaluations for many CPU/GPU combinations.

[gmx-users] request

can you please email me and tell where i can see response to my question? thank you in advance -- 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

Re: [gmx-users] Atom type SDMSO not found

On 7/29/15 12:48 AM, su wrote: Hello everyone I am doing protein-ligand simulation according to Justin's tutorial. After running gmx grompp command, i encountered following error: Fatal error: Atomtype SDMSO not found. Is this the force field matching problem? because i am not able to find

Re: [gmx-users] Atom type SDMSO not found

On 7/29/15 12:59 AM, Sun Iba wrote: Here is the generated topology of ligand with PRODRG server, i believe something is wrong with atom typs here; PRODRG COORDS 29 1UNK CLAW 1 1.328 -0.638 -0.151 1UNK CAM 2 1.384 -0.765 -0.049 1UNK SAU 3 1.520

Re: [gmx-users] Fwd: Question about editconf -noc flag

On 7/29/15 2:32 AM, James Lord wrote: Hi all, I have made an oil slab (energy minimized, equilibrated nvt and npt), some of the oil molecules are at the other end (periodicity). https://drive.google.com/open?id=0B0YMTXH1gmQsYmdvQ3huYWtDaGs then I decided to increase the box size in z

Re: [gmx-users] None constraints and l-bfgs.

On 7/29/15 7:30 AM, Dawid das wrote: Dear Gromacs Experts, I am trying to run l-bfgs minimization with following options (apart from others): integrator = l-bfgs ; (other: cg, l-bfgs) constraints = none ; no constraints but I still get a message that l-bfgs does

[gmx-users] None constraints and l-bfgs.

Dear Gromacs Experts, I am trying to run l-bfgs minimization with following options (apart from others): integrator = l-bfgs ; (other: cg, l-bfgs) constraints = none ; no constraints but I still get a message that l-bfgs does not work with constraints so I should

Re: [gmx-users] None constraints and l-bfgs.

2015-07-29 12:36 GMT+01:00 Justin Lemkul jalem...@vt.edu: To turn that off you would need define = -DFLEXIBLE but you should subsequently re-minimize with constraints to avoid weird geometries. I forgot about it. Thank you! Dawid Grabarek -- Gromacs Users mailing list * Please search the