[gmx-users] pdb2gmx "dangling bond" error when trying to make periodically connected DNA

Hi, I'm trying to create a topology for DNA with periodically connected ends. There's a previous message on this, with advice by Justin: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096970.html I have a single-stranded DNA structure in a pdb file with a phosphate on

Re: [gmx-users] umbrella sampling

and i have AA between sheet and wall.and it should get closer to sheet during pulling. How should i set the initial place of amino acid? it should have the minimum interaction with wall and sheet , am i right? On Fri, Feb 2, 2018 at 7:14 PM, Rose wrote: > > > Sent from my

Re: [gmx-users] umbrella sampling

Sent from my iPhone > On Feb 2, 2018, at 19:01, Justin Lemkul wrote: > > > >> On 2/2/18 8:43 AM, rose rahmani wrote: >> Hi, i'm doing umbrella sampling.(pulling AA toward nanosheet).and 4nS >> simulation for each window. >> g_energy -f umbrella0.edr -o out.xvg >> 1

Re: [gmx-users] gmx mdrun, VERSION 5.0.2

Hi, You've been using 5.1.4, not just 5.0.2. Older software can't know details about what newer software does, and the .tpr file format is one of those details. Make your tpr with 5.0.2 Mark On Fri, Feb 2, 2018 at 4:23 PM K. Subashini wrote: > Hi gmx users, > > I use

Re: [gmx-users] gmx mdrun, VERSION 5.0.2

On 2/2/18 10:22 AM, K. Subashini wrote: Hi gmx users, I use GROMACS version 5.0.2 I got the following error, while giving gmx mdrun -nt 8 -v -deffnm NVT.tpr Reading file NVT.tpr, VERSION 5.1.4 (single precision) --- Program mdrun, VERSION

Re: [gmx-users] How to use "gmx editconf -bf" to assign b-factor values to a PDB containing multiple frames?

Hi, Unfortunately there's no infrastructure for that, so you should either consider something like MDAnalysis, or resort to trjconv -dump to get single frames to give to editconf. Mark On Fri, Feb 2, 2018 at 2:02 PM ZHANG Cheng <272699...@qq.com> wrote: > Dear Gromacs, > I am using: > > > gmx

Re: [gmx-users] umbrella sampling

On 2/2/18 8:43 AM, rose rahmani wrote: Hi, i'm doing umbrella sampling.(pulling AA toward nanosheet).and 4nS simulation for each window. g_energy -f umbrella0.edr -o out.xvg 1 Bond 2 Angle3 Proper-Dih. 4 Improper-Dih. 5 LJ-146 Coulomb-14

Re: [gmx-users] How to use "gmx editconf -bf" to assign b-factor values to a PDB containing multiple frames?

On 2/2/18 8:01 AM, ZHANG Cheng wrote: Dear Gromacs, I am using: gmx editconf -f protein.pdb -bf bf.dat -o bf.pdb to assign b-factor values to "protein.pdb", which contains multiple pdb frames. However, the output "bf.pdb" only includes the first frame. Can I ask is there a way to assign

Re: [gmx-users] Heat capacity of the system

On 2/2/18 7:10 AM, Malvika K wrote: I have another query. I have a protein in water system simulated at different temperatures and I wish to calculate the heat capacity of the system. Unfortunately, at some temperatures, I do not have the original .edr files. In search of a way around this

Re: [gmx-users] constant surface tension in gormacs

On 2/1/18 7:35 PM, Ali Shomali wrote: Dear Justin and all GROMACS users, I'm simulating a monolayer system using the surface tension command in gromacs to set the surface tension and obtain the area( per molecule). Although my system is 2d and uniform : a slab of water covered with

Re: [gmx-users] Running long MD simulation

On 2/1/18 12:45 PM, Ahmed Mashaly wrote: Hi I want to run a long MD 200 ns, but I want the outputs of every 5 ns to be saved separately ... Is there a way or a script to do this? Kind Regards,Ahmed It should be very simple with a bash loop and making use of mdrun -noappend so you avoid

Re: [gmx-users] KALP15 in DPPC

On 2/1/18 6:14 PM, negar habibzadeh wrote: hi . I want to measure the distance between center of membrane and a peptide . how can i use gmx distance ?? What have you tried? Did it work or cause problems? -Justin On Wed, Jan 31, 2018 at 8:13 PM, Justin Lemkul wrote:

Re: [gmx-users] simulation of water

On 2/1/18 11:41 AM, Negar Parvizi wrote: Dear all users, I am new to Gromacs and I want to simulate a box of pure water.I want to know is there any tutorial for this simulation with Gromacs? or Could anyone kindly help me? Use gmx genconf -nbox to replicate the existing spc216.gro to

[gmx-users] gmx mdrun, VERSION 5.0.2

Hi gmx users, I use GROMACS version 5.0.2 I got the following error, while giving gmx mdrun -nt 8 -v -deffnm NVT.tpr Reading file NVT.tpr, VERSION 5.1.4 (single precision) --- Program mdrun, VERSION 5.0.2 Source code file:

[gmx-users] umbrella sampling

Hi, i'm doing umbrella sampling.(pulling AA toward nanosheet).and 4nS simulation for each window. >> g_energy -f umbrella0.edr -o out.xvg 1 Bond 2 Angle3 Proper-Dih. 4 Improper-Dih. 5 LJ-146 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 9

[gmx-users] How to use "gmx editconf -bf" to assign b-factor values to a PDB containing multiple frames?

Dear Gromacs, I am using: gmx editconf -f protein.pdb -bf bf.dat -o bf.pdb to assign b-factor values to "protein.pdb", which contains multiple pdb frames. However, the output "bf.pdb" only includes the first frame. Can I ask is there a way to assign b-factor values to all the frames of one

Re: [gmx-users] Heat capacity of the system

I have another query. I have a protein in water system simulated at different temperatures and I wish to calculate the heat capacity of the system. Unfortunately, at some temperatures, I do not have the original .edr files. In search of a way around this problem, I am wondering if I can use mdrun