Re: [gmx-users] Bug?! Lost particles while sorting

Hi Mark, Thanks for replying on this email. I forgot to reply again and mention that it was not a bug. I could fix it simply by following some instructions in: https://docs.computecanada.ca/wiki/GROMACS It is working perfectly fine now (GPU with version 2016.3) Here are two things I changed in

Re: [gmx-users] Order Parameter for HII phase

Hi Justin, Tom, Antonio, I read the articles recommended in the previous emails. To get the order parameter, for any system and by any technique (e.g. g_angle), we need to calculate the C-D vector angle with respect to the "local normal vector" at the place of that lipid. For the bilayer, it is

[gmx-users] Fwd: LINCS WARNING during EPM2 CO2 Energy Min

Dear community members, Recently I'm using GMX 5.1.4 to simulate EPM2 CO2 with virtual sites, while I met continual LINCS WARNING. I've been struggling for more than week but make no progress in fixing it.. : ( Here attach my pdb, top, and mdp files below. I would much appreciate any tip &

[gmx-users] LINCS WARNING during EPM2 CO2 Simulation

Dear community members, Recently I'm using GMX 5.1.4 to simulate EPM2 CO2 with virtual sites, while I met continual LINCS WARNING. I've been struggling for more than week but make no progress in fixing it.. : ( Here attach my pdb, top, and mdp files below. I would much appreciate any tip &

Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

Oh my God,i face with wall at beginning as a BEGINNER ;) I really appreciate you ,sir, for answering my questions patiently,I WILL BACK soon ;) With regards Rose Sent from my iPhone > On Oct 19, 2017, at 1:14, Alex wrote: > > No, what I am saying is that you need

Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

No, what I am saying is that you need to meticulously modify the amber99 forcefield (if that is indeed suitable) to represent your nanosheet. The charges have to come from appropriate sources, whether it's your Gaussian or whatever. This will fix all forcefield-related errors you are encountering.

Re: [gmx-users] (no subject)

Essential Dynamics = extracts the correlated motions of proteins to understand the motions that are most fundamental to the activity of the protein (http://www.gromacs.org/Documentation/How-tos/Essential_Dynamics) Accelerated MD = enhanced-sampling method that improves the conformational space

Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

On 10/18/17 5:14 PM, Rose wrote: Oh,you mean that i should make My sheet then just optimize it(with out putting charge) and then convert it to .pdb file and use it in MD as an input? I have checked the literature the suitable FF was amber99. What Alex is saying is that none of the force

Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

When I use amber99 FF i face error which says: residue NA is not identified in force field database! -- 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] is there any special tutorial for the interaction of nanosheet and amino acids?

Oh,you mean that i should make My sheet then just optimize it(with out putting charge) and then convert it to .pdb file and use it in MD as an input? I have checked the literature the suitable FF was amber99. Different question;) , what is the difference between using vaccum gap (that Will be

Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

Hi Rose, It sounds like a lot of things packed in a very short message, so let me try to clarify a few points: 1. Gromacs is not DFT, it is particle-based. You simulated your nanosheet in Gaussian and it is my understanding that you used CHELPG to obtain the partial atomic charges. 2. Those

[gmx-users] elevation the temperature

Hi Dear all I want to elevate the temperature of my simulation system with the rate of 1 K/ns, so I would like to know which parameter should be changed to elevate the temperature from 300 up to 450 K? thanks a lot best wishes -- *Marzieh DehghanPhD of BiochemistryInstitute of biochemistry

Re: [gmx-users] .XYZ file format to .gro format

As Justin pointed out in GROMACS per se we can't convert .xyz to .gro file. On 19-Oct-2017 1:32 AM, "Dr. K N Naresh, Post-Doctoral Fellow, Biosciences, SSSIHL" wrote: I can think of an option If it is a small molecule, .xyz can be converted to .pdb using 'OpenBabel'.

Re: [gmx-users] .XYZ file format to .gro format

I can think of an option If it is a small molecule, .xyz can be converted to .pdb using 'OpenBabel'. And .gro file can be generated for the .pdb using PRODRG server online. I guess even directly using the .xyz file, PRODRG can generate .gro file. Best Naresh On 18-Oct-2017 8:53 PM, "Justin

Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

first thank you for your attntion, i made ZnS nanosheet with VNL software,it has 33 atoms,i choosed vaccum gap,then i optimized and charged it with gaussian03,the amino acid is threonin,for the first time i want to study the interaction of these two structures, i am not even sure that my nano

Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

first thank you for your attntion, i made ZnS nanosheet with VNL software,it has 33 atoms,i choosed vaccum gap,then i optimized and charged it with gaussian03,the amino acid is threonin,for the first time i want to study the interaction of these two structures, i am not even sure that my nano

Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

Hi, That would probably depend on the nanosheet material, the particular amino acid, the solvent & ionic strength, temperature, etc, etc. But no, there is no tutorial and yes, a "nanosheet" can be viewed as a ligand. :) I don't know if this helps, but could you please first give us an idea

[gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

Hi I am a beginner user of GROMACS, i want to simulate the interaction of nano sheet with amino acid ,but i dont know what should do, how should i behave with these structures ? is there any tutoroial for interaction of nano sheet and amino acids? is it like protein-ligand tutorial in GROMACS

Re: [gmx-users] .XYZ file format to .gro format

On 10/18/17 11:01 AM, Nagasree Garapati wrote: Hi I have structure of a molecule in .xyz format, is there an option similar to pdb2gmx in gromacs to convert .xyz file to .gro files? Format conversion is done with editconf or trjconv; the fact that one gets a coordinate file at the end of

[gmx-users] .XYZ file format to .gro format

Hi I have structure of a molecule in .xyz format, is there an option similar to pdb2gmx in gromacs to convert .xyz file to .gro files? -- 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] Running MD simulations at a particular temperature

On 10/18/17 9:41 AM, Dilip H N wrote: Justin Sir, Even i am also using Charmm 36FF. So as u have mentioned in previois message, can u kindly suggest then what ate the correct cutoffs..?? And what would be the other modifications that needs to be done in order to incorporate the Charmm FF I

Re: [gmx-users] Running MD simulations at a particular temperature

Justin Sir, Even i am also using Charmm 36FF. So as u have mentioned in previois message, can u kindly suggest then what ate the correct cutoffs..?? And what would be the other modifications that needs to be done in order to incorporate the Charmm FF Thank you Sent with

Re: [gmx-users] Running MD simulations at a particular temperature

On 10/18/17 9:14 AM, Pandya, Akash wrote: So I equilibrated my system at 338.15 K , do I still need to use the simulated annealing option to maintain that temperature? My NPT mdp file is shown below. Simply maintaining a temperature is done by employing a thermostat and reference

Re: [gmx-users] Running MD simulations at a particular temperature

So I equilibrated my system at 338.15 K , do I still need to use the simulated annealing option to maintain that temperature? My NPT mdp file is shown below. title = CHARMM27 A33FabGLY NPT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters

Re: [gmx-users] [gmx-developers] Fw: Fw: Two questions about PME-User in coulombtype

Berk, thanks for your reply. I have Cc this email including your answers to the GMX-User. Regards, Yu > -Original Messages- > From: "Berk Hess" > Sent Time: 2017-10-18 19:56:30 (Wednesday) > To: gmx-develop...@gromacs.org > Cc: > Subject: Re: [gmx-developers] Fw:

Re: [gmx-users] Does GROMACS supports ab initio molecular dynamics simulations?

On 10/18/17 8:21 AM, lxj2586 wrote: Dear GMX Users, I would like to simulate the interactions between graphene oxide sheets and cations, which needs to consider the electronic behavior. Therefore, I plan to use ab initio MD (AIMD) simulations. Could anyone tell me whether GROMACS can do

[gmx-users] Does GROMACS supports ab initio molecular dynamics simulations?

Dear GMX Users, I would like to simulate the interactions between graphene oxide sheets and cations, which needs to consider the electronic behavior. Therefore, I plan to use ab initio MD (AIMD) simulations. Could anyone tell me whether GROMACS can do AIMD? Many thanks for your help!

Re: [gmx-users] Regarding usage of version of CGenFF

On 10/18/17 1:14 AM, Dilip H N wrote: Hello, I was able to generate .str file from CGenFF server, and after this, i am able to convert the .str files into .itp, .prm files etc., successfully by using the cgennff_charmm2gmx.py script. but at the end, i am getting the notes as:- NOTE1: Code

Re: [gmx-users] Regarding non zwitterionic structure to zwitterionic structure while using gmxpdb2gmx

On 10/18/17 6:05 AM, Dilip H N wrote: Hello, I have a neutral glycine molecule [NH2CH2COOH] and if i give gmx pdb2gmx i m getting error as:- Fatal error: Atom HO in residue GLY 1 was not found in rtp entry GLY with 11 atoms while sorting atoms. For a hydrogen, this can be a different