[gmx-users] Separate removal of COM motion

Dear all I am involved in a project where the target systems are lipid bilayers with and without different macromolecules embedded. In the past I did quite a lot of MD simulations of membrane systems always removing the COM motion of lipids and the solvent in separate groups. There are

Re: [gmx-users] difference between force constants in various force field

Hello Dr.Lemkul I get it. Thank you very much for your answer. Regards Azadeh -- This email was Anti Virus checked by Security Gateway. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?

Re: [gmx-users] Electron density using g_density

Thanks, Justin. I will as you recommended. The last approach was described in a book chapter for bilayer simulation. I had difficulty to justify that approach. Cheers, Mohsen On Tue, Jan 16, 2018 at 9:42 AM, Justin Lemkul wrote: > > > On 1/16/18 11:37 AM, Mohsen Ramezanpour

Re: [gmx-users] Electron density using g_density

On 1/16/18 11:37 AM, Mohsen Ramezanpour wrote: Dear Gromacs users, In the man page of g_density for calculation of electron density, it is mentioned that: "The number of electrons for each atom is modified by its atomic partial charge." https://linux.die.net/man/1/g_density In some

[gmx-users] Electron density using g_density

Dear Gromacs users, In the man page of g_density for calculation of electron density, it is mentioned that: "The number of electrons for each atom is modified by its atomic partial charge." https://linux.die.net/man/1/g_density In some publications, it seems the authors just took the atomic

Re: [gmx-users] difference between force constants in various force field

On 1/16/18 10:24 AM, kordza...@aut.ac.ir wrote: Hi every one I have a question I want to obtain topology of carbon nano tube with x2top but I must determine the value of bond strength and angle constant. I think we have a bond carbon-carbon that stretches with a constant force for example

[gmx-users] difference between force constants in various force field

Hi every one I have a question I want to obtain topology of carbon nano tube with x2top but I must determine the value of bond strength and angle constant. I think we have a bond carbon-carbon that stretches with a constant force for example in amber force field this constant is 392459 kj

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

I got it, Thank you very much for all the help! -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 08:46 PM To: "gromacs.org_gmx-users"; Subject: Re: Re: Re:Can I get the fraction

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

On 1/16/18 7:46 AM, ZHANG Cheng wrote: Hi Justin, Thank you very much! The legend is "Total" for the command without -surface and -output. So I feel like if I do a division for the last columns from those two commands, I can just get the fraction of folded/unfolded? Strictly speaking,

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

Hi Justin, Thank you very much! The legend is "Total" for the command without -surface and -output. So I feel like if I do a division for the last columns from those two commands, I can just get the fraction of folded/unfolded? e.g. 1.467/2.767 1.824/2.757 1.901/2.736 ... ...

Re: [gmx-users] six member ring won't stay flat

On 1/16/18 6:38 AM, MD wrote: Hi Justin, I got the itp and parameters of my side chain modified amino acid from CHARMM-GUI and incorporated it into my protein structure, labeled with HETATM. I made the atom types names consistent with charmm forcefield which I used with gromacs and made sure

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

On 1/16/18 7:02 AM, ZHANG Cheng wrote: Hi Justin, Thank you very much. So I tried: gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns -surface 'group 0' -output 'group 1' And got: 0.000 206.8651.467 0.100 232.4501.824 0.200 225.984

Re: [gmx-users] rlist

Hi Mark, I implement a pseudo hard sphere potential, (LJ form potential with powers 50, 49 instead of 12,6), wiht parameter sigma and epsilon parameters and vdW cut-off=sigma. I used Gromacs for this and is working properly for the first step. Do you then have an idea how big should be rlist

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

Hi Justin, Thank you very much. So I tried: gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns -surface 'group 0' -output 'group 1' And got: 0.000 206.8651.467 0.100 232.4501.824 0.200 225.9841.901 ... ... So my understanding

Re: [gmx-users] The official release of GROMACS 2018

Hi, Please start a new email, rather than replying to a digest and confusing the history of the mailing list archive. On Fri, Jan 12, 2018 at 7:05 AM Adarsh V. K. wrote: > In case of Protein-ligand simulation, > > 1) Whether all commands used in GROMACS 5.1.4 is

Re: [gmx-users] NVML library in CUDA 9 & Gromacs 2018

Hi, The default changed in GROMACS 2018 - even if NVML is found, we do not link with it by default. Use cmake -DGMX_USE_NVML=on. Be advised that you may need to take care that the nvml library found at run time is compatible with the CUDA version used at compilation time. That can be non-trivial

Re: [gmx-users] rlist

Hi, That depends on what model you want to implement - rlist sets the radius within which particles/groups will be placed in the neighbour list. There's further requirements based on the other elements of the simulation with which it has to interact, so for user tables, the group scheme is

Re: [gmx-users] six member ring won't stay flat

Hi, You still have many sources of problems (e.g. the warnings you suppressed, the fact that your ring's atoms interact with an environment). What happens when you minimize a capped peptide in vacuo? Mark On Tue, Jan 16, 2018 at 12:39 PM MD wrote: > Hi Justin, > > I got the

Re: [gmx-users] six member ring won't stay flat

Hi Justin, I got the itp and parameters of my side chain modified amino acid from CHARMM-GUI and incorporated it into my protein structure, labeled with HETATM. I made the atom types names consistent with charmm forcefield which I used with gromacs and made sure overall the parameters look decent

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

On 1/16/18 6:19 AM, ZHANG Cheng wrote: Hi Alexandr, Thank you, but it is the same with spaces between | :( I provided the appropriate syntax before: http://manual.gromacs.org/documentation/2018-latest/user-guide/cmdline.html#g-sas -select and -output take strings that select what you want

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

Hi Alexandr, Thank you, but it is the same with spaces between | :( Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 06:37 PM To: "gromacs.org_gmx-users"; Subject: Re:Re: Can

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

On 16/01/2018 11:37, ZHANG Cheng wrote: Hi Justin, thank you very much. Sorry I still do not fully understand. I have an index file, in which the group 0 is all the residue atoms of the protein, group 1 is the first residue atoms. I want to calculate the sasa fraction of the residue 1. The

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

Hi Justin, thank you very much. Sorry I still do not fully understand. I have an index file, in which the group 0 is all the residue atoms of the protein, group 1 is the first residue atoms. I want to calculate the sasa fraction of the residue 1. The fraction means: the sasa at folded state