Re: [gmx-users] Regarding Umbrella sampling

Thanks Justin, Got it -Amir On Wed, Mar 8, 2017 at 7:08 PM, Justin Lemkul wrote: > > > On 3/8/17 8:43 PM, Amir Zeb wrote: > >> Thanks Justin, >> >> The current version I'm working on is 5.0.6, and I don't have access to >> update this version. Can you please let me know how

Re: [gmx-users] Polymer Simulations

Thank you for the reply sir. On Wed, Mar 8, 2017 at 6:13 PM, Justin Lemkul wrote: > > > On 3/8/17 6:13 AM, NIKHIL JOSHI wrote: > >> hii >> >> I am simulating polymer of 100 chains of 12 monomer repeat units. After >> the >> final run, if I observe the final structure in vmd,

Re: [gmx-users] Regarding Umbrella sampling

On 3/8/17 8:43 PM, Amir Zeb wrote: Thanks Justin, The current version I'm working on is 5.0.6, and I don't have access to update this version. Can you please let me know how to get files compatible for this version? You'll either have to translate the appropriate options to the old syntax:

Re: [gmx-users] Regarding Umbrella sampling

Thanks Justin, The current version I'm working on is 5.0.6, and I don't have access to update this version. Can you please let me know how to get files compatible for this version? Regards! -Amir On Wed, Mar 8, 2017 at 5:32 PM, Justin Lemkul wrote: > > > On 3/8/17 8:11 PM,

Re: [gmx-users] Question regarding rebuilding the simulation box

Hi, I don't see any problem, nor how I can guess what mdrun was complaining about. :-) Mark On Wed, 8 Mar 2017 00:13 wrote: > Dear Mark, > > Thanks for your response. Actually, my simulation box contains polarize > water + lipid. So, when I exert editconf

Re: [gmx-users] Regarding Umbrella sampling

On 3/8/17 8:11 PM, Amir Zeb wrote: Hello gmx users, I want to calculate binding energy for a protein-ligand complex. Obviously, this is the very first time, I'm handling umbrella sampling, so I faced the following error. WARNING 2 [file pull.mdp, line 65]: Unknown left-hand 'pull_ncoords'

Re: [gmx-users] Use of -nr for order parameters

On 3/8/17 4:46 PM, Wally Davis wrote: Hi, I'm trying to use the g_order function. I have formated my .ndx file with one group per carbon and provide this file under the -n input option. However, I alway get the error that the -nr file is not found. What is the extra .ndx file I need to

Re: [gmx-users] Question regarding rebuilding the simulation box

On 3/8/17 5:23 PM, ali.khourshae...@student.sharif.edu wrote: Dear Gromacs users, If I want to modify an available simulation box ( 128 DPPC + 2000 W) and change it into a cubic one is the below command true or not? editconf -f Input.gro -bt cubic -box 10 -o Output.gro What happens when

[gmx-users] Regarding Umbrella sampling

Hello gmx users, I want to calculate binding energy for a protein-ligand complex. Obviously, this is the very first time, I'm handling umbrella sampling, so I faced the following error. WARNING 2 [file pull.mdp, line 65]: Unknown left-hand 'pull_ncoords' in parameter file WARNING 3 [file

[gmx-users] Question regarding rebuilding the simulation box

Dear Gromacs users, If I want to modify an available simulation box ( 128 DPPC + 2000 W) and change it into a cubic one is the below command true or not? editconf -f Input.gro -bt cubic -box 10 -o Output.gro Sincerely, Ali -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Use of -nr for order parameters

Hi, I'm trying to use the g_order function. I have formated my .ndx file with one group per carbon and provide this file under the -n input option. However, I alway get the error that the -nr file is not found. What is the extra .ndx file I need to provide? -- Gromacs Users mailing list *

[gmx-users] Use of input -nr to calculate order parameter

Hi, I'm trying to use the g_order function. I have formated my .ndx file with one group per carbon and provide this file under the -n input option. However, I alway get the error that the -nr file is not found. What is the extra .ndx file I need to provide? -- Gromacs Users mailing list *

Re: [gmx-users] Regarding Residue..

I want to simulate a liquid having Charmm FF with inserting a small dipeptide as above FF into it... whn i gave the command gmx pdb2gmx and selected the charmm FF.. I am getting the following error... All occupancies are one Opening force field file

Re: [gmx-users] Invalid Order for Directive Defaults Error Due to Force Field Mixing

Thanks Dr. Justin, Got it -Amir On Fri, Mar 3, 2017 at 5:00 AM, Justin Lemkul wrote: > > > On 3/3/17 1:49 AM, Amir Zeb wrote: > >> Hi Dr. Justin, >> >> I'm wondering that you have mentioned CHARMm27 is not a valid identifier >> of >> protein forcefield, but we have so many

Re: [gmx-users] Question regarding lipid bilayer pore formation

On 3/8/17 8:05 AM, ali.khourshae...@student.sharif.edu wrote: Dear Gromacs users, Based on the previous published papers, I know that a 200bar pressure causes the lipid bilayer to rupture. Therefore I exerted a 200bar equibiaxially to my system and after a while it gave the following error:

Re: [gmx-users] Calculating area per lipid and monolayer thickness

On 3/8/17 8:06 AM, Merril Mathew wrote: I dont know what I am doing wrong. There is no Box-X or Box-Y when prompted. These are the list I get: - 1 Angle2 Proper-Dih. 3 Ryckaert-Bell. 4 Improper-Dih. 5

Re: [gmx-users] Calculating area per lipid and monolayer thickness

I dont know what I am doing wrong. There is no Box-X or Box-Y when prompted. These are the list I get: - 1 Angle2 Proper-Dih. 3 Ryckaert-Bell. 4 Improper-Dih. 5 LJ-146 Coulomb-14 7

[gmx-users] Question regarding lipid bilayer pore formation

Dear Gromacs users, Based on the previous published papers, I know that a 200bar pressure causes the lipid bilayer to rupture. Therefore I exerted a 200bar equibiaxially to my system and after a while it gave the following error: One of the box vectors has become shorter than twice the cut-off

Re: [gmx-users] Calculating area per lipid and monolayer thickness

On 3/8/17 7:52 AM, Merril Mathew wrote: I am not sure what command to use to extract the X and Y box vector. is it gmx energy -f md.edr -o .xvg? Yes. and which option should I choose from the list? The ones I said before, (the aptly named) Box-X and Box-Y. -Justin On 8 Mar 2017 12:44

Re: [gmx-users] Calculating area per lipid and monolayer thickness

I am not sure what command to use to extract the X and Y box vector. is it gmx energy -f md.edr -o .xvg? and which option should I choose from the list? On 8 Mar 2017 12:44 p.m., "Justin Lemkul" wrote: > > > On 3/8/17 7:28 AM, Merril Mathew wrote: > >> I have a system that I

Re: [gmx-users] Regarding Residue..

On 3/8/17 6:18 AM, Dilip H N wrote: I have created a glycylglycine.pdb using avogadro software..and its residue are.. N DGLY A CA DGLY A C DGLY A O DGLY A HA1 DGLY A HA2 DGLY A H DGLY A HN DGLY A N DGLY A CA DGLY A C DGLY A O DGLY A HA1 DGLY A HA2

Re: [gmx-users] Calculating area per lipid and monolayer thickness

On 3/8/17 7:28 AM, Merril Mathew wrote: I have a system that I simulated using GROMACS v5.0.4. The system is two monolayers of lipid on each side of a box of water. I would like to know if there is a way to calculate area per lipid and monolayer thickness. I read that one can use gmx energy to

Re: [gmx-users] Polymer Simulations

On 3/8/17 6:13 AM, NIKHIL JOSHI wrote: hii I am simulating polymer of 100 chains of 12 monomer repeat units. After the final run, if I observe the final structure in vmd, the structure is splitting into two. What will be the reason and how to rectify it. Please

[gmx-users] Calculating area per lipid and monolayer thickness

I have a system that I simulated using GROMACS v5.0.4. The system is two monolayers of lipid on each side of a box of water. I would like to know if there is a way to calculate area per lipid and monolayer thickness. I read that one can use gmx energy to find box size in X and Y and you divide the

[gmx-users] Regarding Residue..

I have created a glycylglycine.pdb using avogadro software..and its residue are.. N DGLY A CA DGLY A C DGLY A O DGLY A HA1 DGLY A HA2 DGLY A H DGLY A HN DGLY A N DGLY A CA DGLY A C DGLY A O DGLY A HA1 DGLY A HA2 DGLY A H DGLY A OXT DGLY A HO DGLY

[gmx-users] Regarding residue ...

I have created a glycylglycine.pdb using avogadro software..and its residue are.. N DGLY A CA DGLY A C DGLY A O DGLY A HA1 DGLY A HA2 DGLY A H DGLY A HN DGLY A N DGLY A CA DGLY A C DGLY A O DGLY A HA1 DGLY A HA2 DGLY A H DGLY A OXT DGLY A HO DGLY

[gmx-users] Polymer Simulations

hii I am simulating polymer of 100 chains of 12 monomer repeat units. After the final run, if I observe the final structure in vmd, the structure is splitting into two. What will be the reason and how to rectify it. Please find the attachment. Thanks in advance -- Gromacs Users mailing list *

[gmx-users] NVE Temperature Drop ONLY When Applying Restraints

Dear Users, I was observing significant temperature drops in my system when switching from NPT equilibration to NVE. Within 1ns of the NVE run the temperature was so low the water was freezing. Trying to understand what was causing it, I have observed that it only occurs when I apply position

Re: [gmx-users] Get a correct .pdb for a synthetic peptide

Hi, I quite often use Avogadro and it always works. Just, remember to change names of the residues/molecules in pdb that they match with topology file. Cheers, Tomasz On 8 March 2017 at 10:36, Sotirios Dionysios I. Papadatos < si.papada...@edu.cut.ac.cy> wrote: > Hi, to get things straight did

Re: [gmx-users] Get a correct .pdb for a synthetic peptide

Hi, to get things straight did you use pdb2gmx or just editconf? Where does the error occur? My personal choice is Maestro which is free for academic use. The resulting pdbs' have no problem with Gromacs. If you want to make minor changes, for example change LIG to DRG (assuming DRG is

[gmx-users] Get a correct .pdb for a synthetic peptide

Hello, I want to run a gromacs MD for a small synthesized peptide. All used amino acids are known for and defined in gromacs, as are the termini. Consequently it would be ideal to use pdb2gmx to create the*.gro, *.top and *.itp, but I have troubles creating a syntactically correct *.pdb input

[gmx-users] Get a correct .pdb for a synthetic peptide

Hello, I want to run a gromacs MD for a small synthesized peptide. All used amino acids are known for and defined in gromacs, as are the termini. Consequently it would be ideal to use pdb2gmx to create the*.gro, *.top and *.itp, but I have troubles creating a syntactically correct *.pdb input