Re: [gmx-users] Free Energy calculation

Hello, Thank you for the quick reply @ Mark Abraham. I am describing in detail what i want to do. I have taken SWCNT (12*12)and encapsulate the molecule. Now i want to check its binding free energy. I checked reference manual to arrange the right order but didn’t success. can anyone have any

Re: [gmx-users] GPU Command

Refer this http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-performance.html I use -ntmpi and -ntomp combination with -gpu_id -- 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] calculating pairwise interactions

Changing these parameters is not good, you may need to refer the forcefield original articles. -- 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] WARNING: Listed nonbonded interaction between particles X and Y at distance

Hi, Make sure your particles have vdw on before you add charge to them. That's usually the cause of this problem. Mark On Mon, Apr 16, 2018, 20:51 faride badalkhani wrote: > Dear all, > I am trying to perform free energy calculations of a small drug in octanol >

[gmx-users] WARNING: Listed nonbonded interaction between particles X and Y at distance

Dear all, I am trying to perform free energy calculations of a small drug in octanol using the GROMACS 5.1.3 software. I built a box of octanol using the following command gmx insert-molecules -ci oct.gro -nmol 125 -box 4 4 4 -o oct_box.gro Followed by steepest descent minimization, 100 ps each

Re: [gmx-users] Definiting protonation in pdb2gmx input

Quoting Justin Lemkul : problem. Please file a bug report on Redmine and include example input files and pdb2gmx syntax you're using. Ok, thanks. Bug posted at https://redmine.gromacs.org/issues/2480 -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Definiting protonation in pdb2gmx input

On 4/16/18 9:44 AM, mhuht...@abo.fi wrote: Quoting Justin Lemkul : I just tested this in GROMACS 2018 and it works fine - if you provide the protonated residue name, pdb2gmx correctly interprets the protonation state. Do you have a use case that fails? Is this behavior

Re: [gmx-users] Definiting protonation in pdb2gmx input

Quoting Justin Lemkul : I just tested this in GROMACS 2018 and it works fine - if you provide the protonated residue name, pdb2gmx correctly interprets the protonation state. Do you have a use case that fails? Is this behavior documented somewhere? I don't seem to find any

Re: [gmx-users] gromos54a7 - topolbuild

On Apr 16, 2018, at 7:57 AM, wrote: > Date: Mon, 16 Apr 2018 06:28:52 -0400 > From: Alex > To: gmx-us...@gromacs.org > Subject: [gmx-users] gromos54a7 - topolbuild > Message-ID: > >

Re: [gmx-users] Gmx_solvate

On 4/16/18 8:51 AM, rose rahmani wrote: Thank you so much. You mean first use gmx solvate, then delete the Sol molecules which i dont need them? Yes. So trjorder can fix the rest, yes? No, but trjconv can save what you want based on an index group from gmx select. -Justin On Mon, 16

Re: [gmx-users] Gmx_solvate

Thank you so much. You mean first use gmx solvate, then delete the Sol molecules which i dont need them? So trjorder can fix the rest, yes? On Mon, 16 Apr 2018, 16:26 Justin Lemkul, wrote: > > > On 4/16/18 5:58 AM, rose rahmani wrote: > > Hi, > > > > I have input structure from

Re: [gmx-users] build virus envelop

On 4/15/18 9:22 PM, sunyeping wrote: Dear everyone, Do you have a tutorial of building a virus lip bilayer envelope with its glycoproteins for MD simulation? Recenetly some MD simulation have done with the envelope  of some viruses such as influenza virus (Reddy et al., 2015) and dengue

Re: [gmx-users] Dihedral Angle Distribution

On 4/16/18 3:07 AM, Anjana Jayasinghe wrote: Dear Gromacs Users, I want to calculate dihedral angle distribution for 9 dihedral angles in aliphatic chain of my molecule. I created the index file giving the command make_ndx -f run.gro -o dihedral.ndxThen  I typed,a C13 a C14 a C15 a C16a C14

Re: [gmx-users] Definiting protonation in pdb2gmx input

On 4/16/18 7:07 AM, mhuht...@abo.fi wrote: One of the recurring questions on the list seems to be how to define residue protonation states non-interactively in pdb2gmx input. The interactive options are a bit of a nightmare to use. Could pdb2gmx be modified to optionally read the residue

Re: [gmx-users] Gmx_solvate

On 4/16/18 5:58 AM, rose rahmani wrote: Hi, I have input structure from my last simulation. The box is 12nm long in Z axis. There is a wall and sheet in z=3 and z=8( so z=~ 0 to 3 and z=~ 8 to 12 is empty) . I want to add solvent between z=3-8. How can i do that? The problem is that i cant

[gmx-users] Definiting protonation in pdb2gmx input

One of the recurring questions on the list seems to be how to define residue protonation states non-interactively in pdb2gmx input. The interactive options are a bit of a nightmare to use. Could pdb2gmx be modified to optionally read the residue types from the PDB file itself? The user

[gmx-users] gromos54a7 - topolbuild

Dear all, I wonder if the topolbuild can provide the gromos 54A7 (gmx54a7) FF? Regards, Alex -- 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 http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Gmx_solvate

Hi, I have input structure from my last simulation. The box is 12nm long in Z axis. There is a wall and sheet in z=3 and z=8( so z=~ 0 to 3 and z=~ 8 to 12 is empty) . I want to add solvent between z=3-8. How can i do that? The problem is that i cant adjust wall and sheet( z coordination) to

[gmx-users] REMD Simulation

Dear all, I am trying to do REMD simulation in different cosolvents. I have generated temperatures using temperature genrating tools but it gives different number of temperatures in different solvents with exchange probability of 0.25. Is it fair to do remd with different replicas? In what way it

[gmx-users] Dihedral Angle Distribution

Dear Gromacs Users, I want to calculate dihedral angle distribution for 9 dihedral angles in aliphatic chain of my molecule. I created the index file giving the command make_ndx -f run.gro -o dihedral.ndxThen  I typed,a C13 a C14 a C15 a C16a C14 a C15 a C16 a C17a C15 a C16 a C17 a C18a C16 a