[gmx-users] simulation single molecule in water

Dear gromacs users, I'm simulating a single molecule in spc water. I'm using a cubic water box which has 3.4 nm size. I got the toplogy of my molecule via PRODRG. After running minimization, NVT , NPT and MD for 10 ns , I checked the density of water ,it was less than the real value (1000 kg m\S-3\

[gmx-users] center of mass and box co-ordinates

Hello Justin sir In your tutorial file for umbrella sampling for Aβ42 protofibril, what was the criteria used to determine the coordinates of center of mass and box size which you have takes as editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box 6.560 4.362 12 -- Thanking Y

Re: [gmx-users] keeping water (entirely) out of the bilayer core

Hi Chris, Just think of another possible way without modifying the code. The task can be achieved by increasing the LJ repulsion term between the lipid tail atoms and water molecules, but keeping all other interactions unchanged. To do so, the free energy code can be used. You can create a st

[gmx-users] mdrun-gpu error message on Gromacs 4.5.5

Hi, I am running mdrun-gpu on Gromacs 4.5.5 (with OpenMM). This is my first time using a GPU. I get the following error message when attempting to run mdrun-gpu with my .tpr file: --- Program mdrun-gpu, VERSION 4.5.5 Source code file: /usr/lo

[gmx-users] RE: keeping water (entirely) out of the bilayer core

Chris, not entirely sure if would work, but what about set of particles located at the center of the bilayer (might require anchoring/freezing) which only interacts (via repulsion only) with water, and setting the interaction such that it manages to exclude it from the bilayer region you require

Re: [gmx-users] Proteins with ADP & ATP cofactors

Dear Stephan, thank you for your reply. I'm performing some test with antechamber for a de-novo parametrization, hope to see some good results with it. > You probably have to do a hand job. Look at the .itp/top files and then the force field parmeters, here's not many atoms, so it would take onl

[gmx-users] Re: About Potential energy calculation

Hi Justin Thanks for your answer. Actually, you are right and that is what I am doing now, but it is really time consuming and it is like double calculating because the potential energy is computed during the MD. Any way thanks John Michael -- View this message in context: http://grom

Re: [gmx-users] About Potential energy calculation

On 5/6/13 5:58 PM, jhon michael espinosa duran wrote: Hi all I am doing an NVE simulation of a protein immersed in water, and I want to keep track of the potential energy in the protein. Do you know how can I do it?. I tried saving the energy of the protein ( the protein as an energy group)

[gmx-users] About Potential energy calculation

Hi all I am doing an NVE simulation of a protein immersed in water, and I want to keep track of the potential energy in the protein. Do you know how can I do it?. I tried saving the energy of the protein ( the protein as an energy group) in the .edr file, but when I checked the file with g_en

Re: [gmx-users] REMD Statistics

On Mon, May 6, 2013 at 3:48 AM, Kong xq wrote: > Hi Mark, > > > Thanks for your great help. I am sorry for the negligence to state the > variation value correctly( it should be 0.011 rather than 0.11). Does this > somewhat small value indicate the generalized equilibrium achieved? It might be

Re: [gmx-users] Still having issues analyzing normal-mode hessian

On 5/6/13 2:16 PM, Bryan Roessler wrote: Hello, I have successfully generated a 945MB mtx hessian storing the normal modes of a ~1500AA protein using mdrun with the "nm" integrator and no cutoffs. However, when I try to analyze the normal modes and create trajectories using g_nmeig, I can't se

[gmx-users] Still having issues analyzing normal-mode hessian

Hello, I have successfully generated a 945MB mtx hessian storing the normal modes of a ~1500AA protein using mdrun with the "nm" integrator and no cutoffs. However, when I try to analyze the normal modes and create trajectories using g_nmeig, I can't seem to generate any output. I am running g_nme

Re: [gmx-users] random seed in molecular dynamics

Google knows a lot more about that one than me ;-) Mark On Mon, May 6, 2013 at 9:16 AM, Preeti Choudhary < preetichoudhary18111...@gmail.com> wrote: > hey thanks Mark > What do you mean by -the random seed is in a different variable.Can you > please explain "the random seed" > > > > On Fri,

[gmx-users] Can Gromacs do oscillatory shear?

Hi all, I am trying to preform oscillatory shear flow on Gromacs. Is there any existing commands/codes to do it or do I have to modify the code myself? If I have to modify code, where can I find the source code for deform? Thank you so much! Shirley Young -- gmx-users mailing listgmx-use

Re: [gmx-users] Tryptophan and tyrosine protonation

Please use informative subject lines. "No subject" often gets flagged as spam, and thus people who may be able to help you may never see your message. On 5/6/13 7:58 AM, Sathish Kumar wrote: I want to do simulation of protein at pH 12 so i have to deprotanate tyrosine,tryphtophan.Can you ple

Re: [gmx-users] correct traj for water/ions density

On 5/6/13 7:32 AM, gromacs query wrote: Dear Justin, You don't need to change the trajectory in any way to do density measurements I read sometime before in some paper: water density falls around polymer (COM) at a distance nearly 4.5nm when it is in box of 10x10x10 nm. I assume the polymer

[gmx-users] (no subject)

I want to do simulation of protein at pH 12 so i have to deprotanate tyrosine,tryphtophan.Can you please tell me how i can do with pdb2gmx command -- regards M.SathishKumar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the a

Re: [gmx-users] Reax force field

Thank you sir On Mon, May 6, 2013 at 4:38 PM, Justin Lemkul wrote: > > > On 5/6/13 6:51 AM, Sathish Kumar wrote: > >> hai >> i would like to use Reax force field,can we use reax force field >> in gromacs and if any one please tell to me weather reax ff is useful for >> protein >> >> >

Re: [gmx-users] Thiolate cysteine

Thank you sir On Mon, May 6, 2013 at 4:39 PM, Justin Lemkul wrote: > > > On 5/6/13 7:03 AM, Sathish Kumar wrote: > >> I want to do simulation of protein at pH 12, in this case experimentally >> reported that the disulphide bonds of protein was broken and sulphurs >> become S negative . Can y

Re: [gmx-users] correct traj for water/ions density

Dear Justin, >> You don't need to change the trajectory in any way to do density measurements I read sometime before in some paper: water density falls around polymer (COM) at a distance nearly 4.5nm when it is in box of 10x10x10 nm. I assume the polymer must be near the center of box so 5nm on e

Re: [gmx-users] Thiolate cysteine

On 5/6/13 7:03 AM, Sathish Kumar wrote: I want to do simulation of protein at pH 12, in this case experimentally reported that the disulphide bonds of protein was broken and sulphurs become S negative . Can you please tell me making of disulphide as S- and S- is it correct and how to set fo

Re: [gmx-users] Reax force field

On 5/6/13 6:51 AM, Sathish Kumar wrote: hai i would like to use Reax force field,can we use reax force field in gromacs and if any one please tell to me weather reax ff is useful for protein It won't be easy to use Reax, if it's even possible. You would have to make some serious

Re: [gmx-users] (no subject)

I really don't think thats possible at the moment. All interactions in Reax, if I recall correctly, are dependent on bond order, which is not an implemented concept in gromacs. Erik On 6 May 2013, at 12:51, Sathish Kumar wrote: > hai > i would like to use Reax force field,can we use r

[gmx-users] (no subject)

I want to do simulation of protein at pH 12, in this case experimentally reported that the disulphide bonds of protein was broken and sulphurs become S negative . Can you please tell me making of disulphide as S- and S- is it correct and how to set force field to this.

[gmx-users] (no subject)

hai i would like to use Reax force field,can we use reax force field in gromacs and if any one please tell to me weather reax ff is useful for protein -- regards M.SathishKumar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Pleas

Re: [gmx-users] correct traj for water/ions density

On 5/6/13 4:21 AM, gromacs query wrote: Dear All, I want to calculate water and ions density around polymer. After MD I see my polymer goes near the edges of box and rather some part is out of box. So in order to calculate water and ion density I think polymer should be near the center of box

[gmx-users] Re: correct traj for water/ions density

Sorry forgot to add::: by doing this I can see my polymer near the center of box On Mon, May 6, 2013 at 11:21 AM, gromacs query wrote: > Dear All, > > I want to calculate water and ions density around polymer. After MD I see > my polymer goes near the edges of box and rather some part is out of

[gmx-users] correct traj for water/ions density

Dear All, I want to calculate water and ions density around polymer. After MD I see my polymer goes near the edges of box and rather some part is out of box. So in order to calculate water and ion density I think polymer should be near the center of box (please correct me if wrong) So by doing th

Re: [gmx-users] constant protonation state MD

Then there is a wealth of papers that describe secondary structure determination from the experimental point of view that you should look for. NMR and CD would be the first obvious methods that come to mind, but there are probably others as well. These should be able to help you validate or inval

[gmx-users] Equilibrated system explodes after ~200ns?

Hi all, My simulation is composed of 2 protein chains wrapped around a lipid disk composed of a dozen different lipid types, water and ions in a 15nm cube. The protein encircles the mixed composition lipid disk. I've got 4 duplicate simulations with velocities generated from a different random seed

Re: [gmx-users] random seed in molecular dynamics

hey thanks Mark What do you mean by -the random seed is in a different variable.Can you please explain "the random seed" On Fri, May 3, 2013 at 1:32 PM, Mark Abraham wrote: > gen_vel controls the generation of random velocities. grompp follows it > (but I'd have to check the code to see wha