Re: [gmx-users] Problem in PCA of protein ligand system

Dear Tsjerk Thank you for the suggestion. Best Regards Ashutosh On Mon, Sep 26, 2016 at 7:37 PM, Tsjerk Wassenaar wrote: > Hi Ashutosh, > > If you want to look at specific motions, like a dihedral, then just look at > that (gmx angle). > > Cheers, > > Tsjerk > > On Mon, Sep

Re: [gmx-users] Protein Drug simulation Parameters

I have modified the trajectory running the trjconv command in three steps. First trjconv is with -pbc whole, second is -pbc nojump with respect to first frame and third is centering the the protein and drug. the output of first step is provided as input in the second step and so on. When I am

[gmx-users] want to post question

Hi, I need help to install GROMACS 5.1.4 so I should post some questions. this is my mail : tapaarna...@yahoo.fr -- 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

[gmx-users] GROMACS 5.1.4 Installation problem.

Hi, I have downloaded the GROMACS 5.1.4 but I have all the problems to install it. I am very new in this computer language. I have managed to install a borland C/C++ compiler 5.5 following a video on youtube and now I am struggling with the installation of the Cmake. All the videos I found are

[gmx-users] energy minimization

Dear gromacs users, I have done simulations for 100ns. I would like to do energy minimization by using trajectory file which I got after production phase. Can I do energy minimization passing the trajectory file to -c argument? If it is yes, then tell me how to do it. Thanks in advance Surya

Re: [gmx-users] Negative pressure in an interface NVT simulation

Hi Surya, I don't think you have a gas phase of any kind, your model of water should not produce any appreciable amount of vapor above the liquid slab (as a matter of fact, I think that if you see water molecules in the gas phase using SPC/E and other similar models at 298 K you most likely did

[gmx-users] 1-4 interaction parameters in GROMOS 54a7

Hi all, Does anyone know how to generate the 1-4 interaction parameters (c6 and c12) in gromos 54a7 FF? Is there any reference about that? Thanks! Yours sincerely, Faust -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

Re: [gmx-users] Negative pressure in an interface NVT simulation

How long is your simulation? Is it possible that it has not reached equilibrium yet? Evan L. On Tue, Sep 27, 2016 at 8:02 AM, Surya Prakash Tiwari wrote: > Hello again, > > Can someone take my question. You don't need to fully answer my question. > If you could just show me

[gmx-users] Using flags to debug gromacs

Hello, I would like to know how to pass debugging flags when I build gromacs so that I can see the variables that are been passed when the run gets stuck by using a debugger such as DDT. Can one use DDT with gromacs? I tried in the build directory: cmake .. -DGMX_BUILD_OWN_FFTW=ON

Re: [gmx-users] CMAKE compilation error

On 9/27/16 12:44 PM, Steve Seibold wrote: Thanks for your response. I have attached the files you asked forThe "Cmake_Screen.output" contains, at start, my cmake input command The mailing list does not accept attachments. Either copy-paste the text or upload files to a

[gmx-users] CMAKE compilation error

Thanks for your response. I have attached the files you asked forThe "Cmake_Screen.output" contains, at start, my cmake input command -Steve On 9/20/16 2:52 PM, Steve Seibold wrote: > Hello > I am attempting to compile Gromacs 5.0.4 mpi version and I get the statement > that the

Re: [gmx-users] Negative pressure in an interface NVT simulation

Hello again, Can someone take my question. You don't need to fully answer my question. If you could just show me the direction, that would be more than enough. Thanks in advance. Surya Prakash Tiwari On Wed, Sep 21, 2016 at 12:11 PM, Surya Prakash Tiwari wrote: > Dear

Re: [gmx-users] Protein Drug simulation Parameters

On 9/27/16 7:32 AM, tasneem kausar wrote: Thank you Justin for your reply. There is another question regarding MMPBSA energy calculations. I have calculated the MMPBSA energy of 8 potential protein+drug complex. Simulation time was 50 ns. One of the protein drug complex gives the positive

Re: [gmx-users] Protein Drug simulation Parameters

Thank you Justin for your reply. There is another question regarding MMPBSA energy calculations. I have calculated the MMPBSA energy of 8 potential protein+drug complex. Simulation time was 50 ns. One of the protein drug complex gives the positive binding energy. Does the periodic boundary

Re: [gmx-users] typeB in FEP calculations

On Tue, 27 Sep 2016 11:08:45 +0100 Rui Neves wrote: > However, what I would like to know is: > At the beggining of the topology I call for all the bonded terms > ('#include ffbonded.itp), and then in the [ atoms ] section, I > specify the massB, typeB and chargeB for the

Re: [gmx-users] typeB in FEP calculations

Hi Billy, Thank you so much for the papers you suggested. I hadn't come across them. However, what I would like to know is: At the beggining of the topology I call for all the bonded terms ('#include ffbonded.itp), and then in the [ atoms ] section, I specify the massB, typeB and chargeB for

[gmx-users] deformation of a bilayer

Hi I have built a bilayer with different lipids and now I want to apply a deformation (strain) along the x axis of the box using the deform option . but when I give the grompp , it gives me a fatal error for different reasons everytime I change something in the mdp  file . I dont know much

Re: [gmx-users] Center-of-Mass motion removal setting for Membrane system with multiple peptides.

Actually, I am really not sure whether diffusion out of the box will affect the results or not. As long as the system is able to correctly simulate the intended biological phenomenon i.e. interaction of peptides with membrane, it is fine. Intuitively, one may say that for a semi-isotropic membrane

Re: [gmx-users] Center-of-Mass motion removal setting for Membrane system with multiple peptides.

Hi Abhi, No, restricting the COM motion of the entire system is perfectly fine in most cases. From the conservation of momentum, the COM should not change its velocity at all. One reason the COM motion needs to be kept at bay explicitly is because the accumulation of numerical error during the

Re: [gmx-users] Center-of-Mass motion removal setting for Membrane system with multiple peptides.

Another thing which I don't understand is in case of the peptide group, which I expect to diffuse freely, would COM motion removal be non physical? The starting system has 16 peptides added to one side of the membrane. Now to allow the peptides to diffuse freely and interact with the membrane, I

Re: [gmx-users] Center-of-Mass motion removal setting for Membrane system with multiple peptides.

What I meant to ask was a way to ensure that the peptides and membrane COM don't drift out of the simulation box, but the peptides should be free to move ( relative to the membrane) within the box. Basically, the best way to simulate the diffusion and subsequent interaction of the peptides with

Re: [gmx-users] Center-of-Mass motion removal setting for Membrane system with multiple peptides.

> On 27 Sep 2016, at 06:26, Abhi Acharya wrote: > > Dear Gromacs users, > > I am trying to perform a simulations of different concentration of peptides > in a box with lipid bilayer. In this context, I had a query regarding the > correct Center-of-Mass removal