[gmx-users] About the possibility of calculating dipole moment vectors of individual waters around polar solutes

Hi everyone, I want to visualize how the dipole moment vectors of waters are aligned around certain polar solutes. Can I select the waters to an index file and give that to gmx dipoles to calculate dipole moment components of waters and thus calculate the individual dipole moment vector of each

[gmx-users] How to create parameters for polyethyleneglycol (PEG) 6000 in a gromacs MD simulation

Hi all, I have to carry out MD simulations involving PEG 6000 molecules. When I first build this it is a very long (~480 Angstrom) linear chain. I have the bond/angle/dihedral parameters for this linear structure. Usually when I introduce a non-standard residue, I perform an optimization in

Re: [gmx-users] From: Graduate Student protein active site inquiry

Hi, groups can be specified using gmx select http://biophysics.med.jhmi.edu/~yliu120/tutorials.html and gmx make_ndx http://bioinf.modares.ac.ir/workshop/md_sep_03_2012/fwspidr_tutor.pdf HTH Sajeewa On Sat, May 6, 2017 at 6:35 AM, Felix Y Yang wrote: > Thanks for the

Re: [gmx-users] Box dimensions in the gro file are not read by GROMACS

dimension is not big enough. I will have to equilibrate the system in a bigger box with a larger y dimension and run the umbrella sampling. Thank you very much for your time. Best, Sajeewa On Wed, Mar 29, 2017 at 11:26 PM, Sajeewa Pemasinghe <sajeew...@gmail.com> wrote: > So if t

Re: [gmx-users] Box dimensions in the gro file are not read by GROMACS

So if the actual distance is 2.3 nm why does GROMACS measure it as 3.58 nm ? On Wed, Mar 29, 2017 at 11:11 PM, Sajeewa Pemasinghe <sajeew...@gmail.com> wrote: > The coordinates of group1 center of mass are 44.466, 23.909,35.035 and > that of group 2 are 67.467,23.994,34.088 a

Re: [gmx-users] Box dimensions in the gro file are not read by GROMACS

The coordinates of group1 center of mass are 44.466, 23.909,35.035 and that of group 2 are 67.467,23.994,34.088 as calculated in VMD . So the distance is 23 A . On Wed, Mar 29, 2017 at 11:05 PM, Sajeewa Pemasinghe <sajeew...@gmail.com> wrote: > Hi Justin, > > Thank you for the

Re: [gmx-users] Box dimensions in the gro file are not read by GROMACS

Hi Justin, Thank you for the prompt reply. I asked a second question correcting the value of 23.0 nm. The distance value is 2.3 nm. On Wed, Mar 29, 2017 at 10:57 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/29/17 2:55 PM, Sajeewa Pemasinghe wrote: > >> Hi ev

[gmx-users] Box dimensions in the gro file are not read by GROMACS (correcting an error in the previous question)

Hi everyone, I have run an equilibration of two linear molecules in a water box with dimensions 117A x 54A x 70A for 150 ns. I am using the equilibrated structures (not the final structure) in the final nanoseconds as starting structures for an umbrella sampling calculation. The problem is that

[gmx-users] Box dimensions in the gro file are not read by GROMACS

Hi everyone, I have run an equilibration of two linear molecules in a water box with dimensions 117A x 54A x 70A for 150 ns. I am using the equilibrated structures (not the final structure) in the final nanoseconds as starting structures for an umbrella sampling calculation. The problem is that

Re: [gmx-users] PMF - US histograms problem

Hi, When I get a region sparsely populated like that, I increase the number of points in that particular region and increase the k value to about 3000 but not more than that. Increasing the k value to something like 2 will result in the distribution getting very narrow and therefore further

Re: [gmx-users] Clarification for the meaning of ncoords in GROMACS 5.0.4 pull code

Thank you very much. I really appreciate your help. On Sun, Mar 26, 2017 at 6:16 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/24/17 1:54 PM, Sajeewa Pemasinghe wrote: > >> Hi, >> >> I have two molecules which are not moving in the z axis due to bei

Re: [gmx-users] Need for a clarification between "umbrella restraints" and value for "ncoords" in GROMACS pull code

Thank you very much. I really appreciate it. On Sun, Mar 26, 2017 at 6:17 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/26/17 8:11 AM, Sajeewa Pemasinghe wrote: > >> Hi all, >> >> I have a system in which I need to maintain the center of mass distan

[gmx-users] Need for a clarification between "umbrella restraints" and value for "ncoords" in GROMACS pull code

Hi all, I have a system in which I need to maintain the center of mass distance between two molecules constant for an umbrella window. The structures are not strictly aligned along an axis as they are the product of an equilibrium simulation.I have the following code. pull = umbrella

[gmx-users] Clarification for the meaning of ncoords in GROMACS 5.0.4 pull code

Hi, I have two molecules which are not moving in the z axis due to being continuous across the periodic boxes. I want to keep the distance between them fixed by pulling along x and y axes. So as I am pulling along x and y axes does my ncoords = 2 ? By going along with this logic as long as my

Re: [gmx-users] Using newly defined residue to neutralize the system

Thank you very much for the information. On Wed, Jan 18, 2017 at 11:27 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/18/17 2:22 PM, Sajeewa Pemasinghe wrote: > >> So it should be monoatomic? Because this ion is a complex ion which has 19 >> atoms. So there w

Re: [gmx-users] Using newly defined residue to neutralize the system

1/18/17 3:04 AM, Sajeewa Pemasinghe wrote: > >> Hi all, >> >> I have an itp file to a new residue MGH. It is an ion with a (+2) charge. >> I >> have included the itp file in the topology file using #include MGH.itp. My >> question is, will I be able to use thi

[gmx-users] Using newly defined residue to neutralize the system

Hi all, I have an itp file to a new residue MGH. It is an ion with a (+2) charge. I have included the itp file in the topology file using #include MGH.itp. My question is, will I be able to use this MGH ion to neutralize my system using "gmx genion" without any further modifications to the

Re: [gmx-users] PMF changing drastically with the number of bins

Dear all, I have made mistake. I didn't compare the value of free energy at the minimum with the plateau value. At all three bin numbers the difference is close to 2 kCal mol-1. So this is solved. Best regards Sajeewa On Mon, Dec 19, 2016 at 1:15 PM, Sajeewa Pemasinghe <sajeew...@gmail.

[gmx-users] PMF changing drastically with the number of bins

Dear all, I am calculating the PMF as the COM distance of two molecules are changing using umbrella sampling ( pull = umbrella ). Each umbrella sampling simulation runs for 50ns. When I calculate the PMF with default (200 bins) settings using gmx wham I get the minimum in free energy of -1.19

Re: [gmx-users] protein ligand complex MD simulation

Hi Ashan, This (from the manual, section 4.3.5) https://dl.dropboxusercontent.com/u/50317782/distance_restraints_gromacs.png or this http://www.gromacs.org/Documentation/How-tos/Distance_Restraints will help. Best, Sajeewa On Thu, Dec 8, 2016 at 5:35 AM, ashan dayananda