Re: [gmx-users] Dynamics only for cavity in molecule.

Hi, I have no idea whether that will help. Even if it is better, I am struggling to see that annealing and freeze groups is a useful model, even with frozen solvent. Mark On Fri, 4 Aug 2017 21:40 wrote: > Well, that means that I need to use the group scheme? > Or I can just

Re: [gmx-users] Dynamics only for cavity in molecule.

Well, that means that I need to use the group scheme? Or I can just add solvent and run the same thing? > Hi, > > I imagine nobody has ever tried with Verlet plus freeze plus annealing, so > it could be broken somehow... But frozen atoms around a cavity and no > electric field from solvent sounds

[gmx-users] error at nvt equilibrium

Dear Sir I am getting the error when I try for *gmx mdrun -deffnm nvt. * I have attached my nvt.mdp. Can anyone help me about it Double sids (1547, 1548) for atom 4837 Double sids (1547, 1548) for atom 4838 Double sids (1547, 1548) for atom 4839 Double sids (1547, 1548) for atom 4840 Double sids

Re: [gmx-users] Dynamics only for cavity in molecule.

Hi, I imagine nobody has ever tried with Verlet plus freeze plus annealing, so it could be broken somehow... But frozen atoms around a cavity and no electric field from solvent sounds like a model highly unlikely to be related to reality... Mark On Fri, 4 Aug 2017 18:55

[gmx-users] Dynamics only for cavity in molecule.

Hello! I want to run dynamics only for a relatively small cavity of my molecule, with all other atoms frozen. For this reason, I also don't use solvent, because it won't move anyway. I run the simulation on GPU (gromacs 5.1.2), i.e. I use the Verlet scheme, pbc = xyz. However, when I start

[gmx-users] MnO2 periodic system

Dear all, I am trying to equilibrate a MnO2 surface (not cluster periodic). After the NVT run, I see that the surface is deformed. I was wondering what else can I add in my nvt.mdp to not encounter this problem? I have mainly followed the examples in the forum for graphene/CNT growth. title

Re: [gmx-users] question about gmx do_dssp

Hi, Isn't that figure what is in the xpm file? Mark On Fri, Aug 4, 2017 at 4:20 PM YanhuaOuyang <15901283...@163.com> wrote: > Hi, >I have run a MD simulation and used gmx do_dssp to calculate the > secondary structure content. The output files are md_dssp.xpm and > scount.xvg. I want to

Re: [gmx-users] Problem with dihedral restraints

Hi, You should expect changes, you're not freezing the angles in place. You're making it less energetically favourable for them to change. But if the environment is strong enough, they'll respond to that. Increase kfac by a factor of a thousand and they'll probably not move noticeably. Whether

Re: [gmx-users] Problem with dihedral restraints

Thank you for the kind reply. I will compute and update in the post. *Thank you* *Gangotri Dey* Postdoctoral Associate Rutgers University New Brunswick Chemistry and Chemical Biology 174 Frelinghuysen Road, Piscataway, NJ 08854 Phone: +16092162254 On Fri, Aug 4, 2017 at 10:31 AM, Mark

[gmx-users] question about gmx do_dssp

Hi, I have run a MD simulation and used gmx do_dssp to calculate the secondary structure content. The output files are md_dssp.xpm and scount.xvg. I want to know that each residue belongs to what kind of secondary structure for each frame. But the scount.xvg output file only have the number

[gmx-users] Problem with dihedral restraints

Hello! I posted a question a few days back and I got a reply but it still does not work. I have a small drug molecule that I would like to compute. I want to restraint the Ramachandran dihedral angles. I have used the following lines in the .itp file for the molecule. It was suggested that I

Re: [gmx-users] Error in itp file

You can use this link for ACPYPE: http://webapps.ccpn.ac.uk/acpype/ First, you have to mail the author and then he would give you a user ID and password. On Fri, Aug 4, 2017 at 1:48 AM, Justin Lemkul wrote: > > > On 8/3/17 8:53 AM, Souvik Dey wrote: > >> ​Yes, I saw the

[gmx-users] Could not find clayff forcefield

Dear users, I try to implement Clayff forcefield for Kaolinite. I created my force field (I'm not sure about it), but gromacs couldn't find my force field in the directory. Here is my forcefield. ffnonbonded [ atomtypes ] ; name mass chargeptype sigma eps HW 1

[gmx-users] The small organic molecule occurred deformation during simulation

Hello, users I’m a novice to study the gromacs program. Now I met some problems which the small molecule occurred deformation when energy minimization was performed. For example, the anthracene molecule became bent in the plane of C-rings, the same as phenol. I want to know whether the

Re: [gmx-users] Does gmx distance correct for broken molecules from pbc?

Hi, gmx help distance shows that there are two PBC-related options. Perhaps your answer lies there. Mark On Fri, Aug 4, 2017 at 9:47 AM Ramon Crehuet wrote: > Dear all, > > I have a system composed of a trimeric protein and a double stranded DNA. > I would like to

[gmx-users] Does gmx distance correct for broken molecules from pbc?

Dear all, I have a system composed of a trimeric protein and a double stranded DNA. I would like to calculate the distance between the center of mass (com) of the protein and the com of the DNA (I am working with the NVT equilibration trajectory as an example). I tried: gmx distance -f