Re: [gmx-users] Question on energygrps setting

how can I use the energy grps option for analysis. You would specify groups (with an index file or from default groups) e.g. energygrps = SOL Surface -Justin Thanks Devargya Chakraborty On Thu 7 May, 2020, 8:23 PM Justin Lemkul, wrote: On 5/7/20 10:49 AM, Devargya Chakraborty wrote:

Re: [gmx-users] Question on energygrps setting

ing a matching .tpr with convert-tpr, and then using mdrun -rerun to recompute the energies. While you *can* do this, note that these values will generally have no physical meaning. -Justin Thanks Devargya Chakraborty On Thu 7 May, 2020, 5:48 PM Justin Lemkul, wrote: On 5/6/20 6:31 PM, Lei

Re: [gmx-users] Info regarding restrained minimization, equilibration & production

On 5/7/20 8:53 AM, Paolo Costa wrote: Dear Justin that means when I generate the topology file by pdb2gmx I will add manually the section [constraints] on it? I suggest you look into the manual to understand different ways of applying constraints. You can either convert bonds into constrai

Re: [gmx-users] Info regarding restrained minimization, equilibration & production

Thanks a lot. Paolo Il giorno gio 7 mag 2020 alle ore 14:44 Justin Lemkul ha scritto: On 5/7/20 8:41 AM, Paolo Costa wrote: Dear Justin, thanks a lot for your valuable information. The system (Keggin anion, POM) I am trying to simulate is almost identical to the one already studied in

Re: [gmx-users] Info regarding restrained minimization, equilibration & production

On 5/7/20 8:41 AM, Paolo Costa wrote: Dear Justin, thanks a lot for your valuable information. The system (Keggin anion, POM) I am trying to simulate is almost identical to the one already studied in literature (doi: 10.1021/jp077098p). In the SI of this work, the authors stated "*Keggin anio

Re: [gmx-users] Info regarding restrained minimization, equilibration & production

On 5/6/20 11:35 AM, Paolo Costa wrote: Dear Gromacs users, I am interested on studying the interaction between large metal cluster anions (polyoxometallates, POM) with different organic cations (e.g perylenes, etc..) in water. I have already the non bonded parameters of POMs from literature,

Re: [gmx-users] Question on energygrps setting

On 5/6/20 6:31 PM, Lei Qian wrote: Dear users, I know interaction energy calculation is carried out via energygrps setting in mdp file. Because free energy-related settings do not include this energygrps setting, so I think this energygrps setting may NOT be related to free energy settings. C

Re: [gmx-users] Need help creating md.mdp for silica(quartz)?

On 5/7/20 4:24 AM, Ekatherina O wrote: Hello Dr. Dallas Warren, Thank you for the suggestions. But this does not solve the problem of the movement of atoms of quartz layers (upper and lower) located at the borders of the box. I would like the quartz layers to remain intact during the modelin

Re: [gmx-users] How to apply position restrain on selected atoms in .gro files in Gromacs?

On 5/5/20 5:54 PM, Debashish Banerjee wrote: Dear gmx users, I have been stuck in a problem for a month now and have scrutinized all the past discussions and forms related to it dating as back as 9 years. Now I really need your help. My system has Clays (layered philosillacates), Cesium ions

Re: [gmx-users] [gmx users] Terminal amide hydrogens not included in H-bond analysis

On 5/5/20 12:12 PM, Neena Susan Eappen wrote: Thank you Sahil, I will try VMD plugin for H-bond analysis. Thank you Justin for your reply, it looks like gmx hbond considers only one N-H as donor when part of NH2 group. Please take a look at this file. This is what gmx hbond does by default,

Re: [gmx-users] apply protonation state CYS amino acid

On 5/4/20 11:46 PM, azadeh kordzadeh wrote: Hi Thank you very much for your answer to my former question I want to select CYSH state but we have this option for this amino acid. already I could determine especial state for his,lys,arg,asp by command -his but this command doesn't work for CYS

Re: [gmx-users] about how to create angle.index with specific angles

On 5/2/20 3:12 PM, lazaro monteserin wrote: Dear Dr. Lemkul I used the following protocol to generate the (.xpm) files: I followed the protocol in gromacs website to do dihedral Principal Component Analysis: 1) Created an index file (*dangle.ndx*) with a list of the dihedrals to analyze from

Re: [gmx-users] Redmine posting forbidden?

On 5/2/20 12:13 PM, Eugene Radchenko wrote: Hello, I wanted to report a bug using the Redmine site. Unfortunately, even after registering, the option to submit an issue is missing from the Issues page (where I expected it). While the “File a new issue” link from the main page to https://redm

Re: [gmx-users] Warning: Short Bond pdb2gmx (Justin Lemkul)

On 5/2/20 8:21 AM, Sadaf Rani wrote: Dear Justin I want to get the equilibrium value for bond, angle and dihedral restraints to use in free energy calculation as mentioned in:- https://pubs.acs.org/doi/abs/10.1021/jacs.6b11467 Looking forward to your kind suggestions, please. You can comput

Re: [gmx-users] disulfide bridges

On 5/2/20 6:54 AM, Miro Astore wrote: Hi all, I'm trying to make a protein with a fair few disulfide bridges and I couldn't get it to work. I chose -ss yes and increased the minimum distance in specbonds.dat but it doesn't seem to want to let me see all possible pariings. specbond.dat does

Re: [gmx-users] Warning: Short Bond pdb2gmx

On 5/1/20 2:41 PM, Sadaf Rani wrote: Dear Gromacs users I did 50ns MD simulation of a protein-ligand complex. From this trajectory, I extracted region of trajectory having stable rmsd and generated an average structure. I want to run this average structure to get an idea of setting some restra

Re: [gmx-users] PBC after energy minimization

On 5/1/20 9:29 AM, John Whittaker wrote: Hi Mohamed, Hello everybody, In order to solve the PBC at the end I use the command: *gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_noPBC.xtc -pbc mol * followed by: *gmx trjconv -s md_0_1.tpr -f md_noPBC.xtc -o md_noPBC.pdb* I want to solve th

Re: [gmx-users] about how to create angle.index with specific angles

advance, Lazaro On Wed, Apr 29, 2020 at 8:57 PM Justin Lemkul wrote: On 4/29/20 7:11 PM, lazaro monteserin wrote: Dear Dr. Lemkul it could be possible use that angle.index with the selected dihedrals written by hand as index file for gmx angle for dihedral Principal Component Analysis

Re: [gmx-users] Invalid atomtype format (Justin Lemkul

On 4/30/20 7:10 AM, Sadaf Rani wrote: Dear Justin I have removed the blank lines but getting a new warning while doing gmx pdb2gmx:- WARNING: Duplicate line found in or between hackblock and rtp entries I am not getting what else is wrong. Could you please help me to figure out. I have shar

Re: [gmx-users] Invalid atomtype format (Justin Lemkul)

On 4/29/20 7:41 PM, Sadaf Rani wrote: Dear Justin I have shared the files for the users mailing list on the following link. https://www.dropbox.com/s/bfaq8z8iqojdm0r/Atom_type_error%20files.zip?dl=0 Remove the blank lines from the end of atomtypes.atp and it works fine. Note that you shoul

Re: [gmx-users] about how to create angle.index with specific angles

want to perform. -Justin Kindly, Lazaro On Wed, Apr 29, 2020 at 7:23 PM Justin Lemkul wrote: On 4/29/20 5:01 PM, lazaro monteserin wrote: Dear gromacs users, Is there any way to tell gmx mk_angndx to create the index file with dihedral angles from a (.tpr) for specific atom numbers (atom

Re: [gmx-users] about how to create angle.index with specific angles

On 4/29/20 5:01 PM, lazaro monteserin wrote: Dear gromacs users, Is there any way to tell gmx mk_angndx to create the index file with dihedral angles from a (.tpr) for specific atom numbers (atom level, e.g 1, 2, 3) from my molecule? mk_angndx is designed for distributions of similar angles

Re: [gmx-users] POPC: Fatal error:

On 4/29/20 8:50 AM, Dutta, Kunal wrote: Dear Friends, I'm trying to learn Tutorial 2: KALP15 in DPPC The FOLLOWING PROBLEM APPEARS: " GROMACS: gmx grompp, version 2018.1 Executable: /usr/bin/gmx Data prefix: /usr Working dir

Re: [gmx-users] Atom positions change between topology generation and NVT equilibration

On 4/29/20 7:49 AM, Max Winokan wrote: My apologies for the missing images. Hopefully they are available along with the MDP in the following link: https://www.dropbox.com/sh/dnqz7c049f4tvw3/AAAGGZ8AF-ddQpBjD-QVf0OAa?dl=0 If anyone knows what could be going on, please let me know. Essen

Re: [gmx-users] Invalid atomtype format

On 4/28/20 11:52 AM, Sadaf Rani wrote: Dear Gromacs users I am facing a problem between different versions of gromacs for gmx pdb2gmx. I have a protein-ligand system, I did all the necessary steps mentioned in gromacs manual for adding new residue to force field. When I run this in gromacs 201

Re: [gmx-users] Segmentation fault (core dumped) error during minimization

On 4/28/20 5:08 AM, Elham Taghikhani wrote: Hi As you said I checked my structure for any bad contact, but the close atoms are part of the protein so I can't delete them to minimize the structure. And water molecules are not that much close to make bad contact with the atom. And the atom whic

Re: [gmx-users] [gmx users] Terminal amide hydrogens not included in H-bond analysis

On 4/27/20 9:50 PM, Neena Susan Eappen wrote: Hello gromacs users, My peptide has an amide group at the C-terminus. Hydrogen bond analysis using gmx hbond does not take into account H-bond donors (NH2) from the amide group (Note: this NH2 is considered as a residue according to opls ff). Wh

Re: [gmx-users] Atom CA used in that entry is not found in the input file

On 4/26/20 4:45 PM, Daniel Burns wrote: Hello, I edited a few selenomethionine residues, changing "S" to "SD" and removed the "SE" at the end of the line. I then ran pdb2gmx with Charmm36. I get the following error (not sure why the residue number doesn't match): Fatal error: Residue 324 n

Re: [gmx-users] Quick question: is TIP3P water model available in GROMOS54a7 force field?

On 4/27/20 7:43 PM, shakira shukoor wrote: Hi As far as I know tip3p water model is modelled to use in combination with CHARMM force field. However there is nothing wrong in using TIP3P in combination with GROMOS force field. And u will have both the bonded and non bonded parameters of that sp

Re: [gmx-users] Error No default Proper Dih. types

ks again. Paolo Il giorno dom 26 apr 2020 alle ore 20:33 Justin Lemkul ha scritto: On 4/26/20 2:08 PM, Paolo Costa wrote: Dear Justin, thanks a lot for your quick reply and useful information. Thus, I will go through to all the dihedral terms and define zero the corresponding force constant as y

Re: [gmx-users] Error No default Proper Dih. types

and angles in terms of internal parameters. -Justin Thanks again. Paolo Il giorno dom 26 apr 2020 alle ore 20:03 Justin Lemkul ha scritto: On 4/26/20 1:57 PM, Paolo Costa wrote: Dear Gromacs users, within Amber99 force field I created a new molecule, polyoxometallate, by creating a new .rt

Re: [gmx-users] Error No default Proper Dih. types

On 4/26/20 1:57 PM, Paolo Costa wrote: Dear Gromacs users, within Amber99 force field I created a new molecule, polyoxometallate, by creating a new .rtp file and modifying the atomtypes.atp, ffnonbonded.itp and the ffbondend.itp. For the ffnonbonded.itp I took the LJ parameters from known work

Re: [gmx-users] Fatal error pdb2gmx

On 4/26/20 5:15 AM, Paolo Costa wrote: Dear Gromax users, I created a new residue of 118 atoms within Amber99 force field. However when I run the "pdb2gmx" I got many times the following warning: "*WARNING: Duplicate line found in or between hackblock and rtp entries" *and in the end I got th

Re: [gmx-users] Why there is no phosphorous atom in the "DA5" residue in dna.rtp

On 4/25/20 12:18 PM, Tingguang.S wrote: Dear all, When I generated the amber99sb force filed topology of a DNA molecule with gmx, a error code appeared: "Atom P in residue DA 1 was not found in rtp entry DA5 with 30 atoms". I tried to fix this but found there was no P atoms in all the

Re: [gmx-users] about error running temperature equilibration

On 4/23/20 3:01 PM, lazaro monteserin wrote: I am trying to run a temperature equilibration of my system and I get the following error: === NOTE 1 [file nvt.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [

Re: [gmx-users] Problem C-H bonds of Benzene after minimization

On 4/23/20 6:52 AM, Paolo Costa wrote: Dear Gromacs Users, I am trying to perform MD simulations of benzene molecule in a cube of water just for practicing. By following the tutorial https://www.svedruziclab.com/tutorials/gromacs/2-methane-in-water/, I setup the residue Benzene within Amber99

Re: [gmx-users] GROMACS mdp file for doing a single point energy after acpype conversion

On 4/23/20 5:42 AM, ABEL Stephane wrote: Deal all, I am using acpype to convert a set of glycolipids modeled with the GLYCAM06 force fiedl into the GROMACS format. acpype works well for this task. But I would like to check if the conversion is correctly done by performing single point ene

Re: [gmx-users] 回复: 回复: Problem with Potential Mean Force calculation

On 4/22/20 10:40 AM, Rolly Ng wrote: Dear Justin and Vu, I think I have solved part of my problem. The number of tpr/xvg pairs were too much in my case. Although I used the script to generate 50 pairs with 0.1nm setting, it turns out that only the first 27 pairs works. What does "only the

Re: [gmx-users] 回复: Problem with Potential Mean Force calculation

uld I check? Thanks, Rolly -邮件原件- 发件人: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 代表 Justin Lemkul 发送时间: 2020年4月21日星期二 下午7:09 收件人: Discussion list for GROMACS users 主题: Re: [gmx-users] Problem with Potential Mean Force calculation On 4/21/20 2:08 AM, Rolly Ng wrote: Dear Gr

Re: [gmx-users] Regarding use of harmonic wall model

On 4/21/20 8:07 AM, Shashank Ranjan Srivastava wrote: Thank you so much Prof. Lemkul for your reply. As I don't know what and how to use this pull code, if you have any idea regarding what you have suggested will be of great help to me. Meanwhile I will read more about it. General principles

Re: [gmx-users] Problem with Potential Mean Force calculation

On 4/21/20 2:08 AM, Rolly Ng wrote: Dear Gromacs user and Dr. lemkul, I think my previous email is too large to send on the list. Could you please kindly look at the link for the plots? https://www.researchgate.net/post/GROMACS_2020_pull_code_produces_strange_Potential_Mean_Force_PMF_resu

Re: [gmx-users] Failed to find GROMACS magic number in trr frame header

On 4/20/20 6:39 AM, Mijiddorj B wrote: Dear Justin, Thank you very much for your reply. I see. I cut trr file several ns before the stopped frame, and I would like to cut the corresponding checkpoint file before the stopped frame. Checkpoint files are not trajectories; they only contain one

Re: [gmx-users] How to solve the "LINCS WARNING" problem (???)

On 4/20/20 3:51 AM, 변진영 wrote: Hi Prasanth Firstly Sorry for late reply… The force field I used is Gromacs 5.x.x 54a7 came from ATB. I downloaded and used the all-atom topology file(.itp) so I said that it is all-atom simulation. By any chance, is it wrong approach?? The GROMOS force

Re: [gmx-users] Segmentation fault (core dumped) error during minimization

On 4/19/20 4:38 PM, Elham Taghikhani wrote: Thank you I corrected the mdp file. As you said I opened my gro file in VMD but I didn't notice any bad contact around the atom. Could you explain how can I observe bad contacts in the structure? Calculate interatomic distances and look for anythin

Re: [gmx-users] about correct methodology to run MD of small molecule in gromacs

PM Justin Lemkul wrote: On 4/19/20 4:12 PM, lazaro monteserin wrote: Dear Dr. Lemkul you are completely right. But then how could I approach this problem to get an answer at the end that make sense? What is the purpose of requiring that the simulation start from the most stable vacuum

Re: [gmx-users] about correct methodology to run MD of small molecule in gromacs

ustin On Sun, Apr 19, 2020 at 4:39 PM Justin Lemkul wrote: On 4/18/20 7:39 PM, lazaro monteserin wrote: Dear Gromacs users, As I have referred before I am simulating small molecules (nucleosides) (around 33 atoms) in vacuum in Gromacs. When I do the simulations at the end I want to select the

Re: [gmx-users] Residue ‘XXX’ not found in residue topology database - SnCl6

On 4/19/20 3:47 PM, Paolo Costa wrote: Hi Justin, I could fix the issue. Thanks again for your help. And in the spirit of helping others that use this mailing list, what exactly was the problem and how did you solve it? -Justin Paolo Il giorno dom 19 apr 2020 alle ore 21:35 Justin

Re: [gmx-users] Failed to find GROMACS magic number in trr frame header

ectly. -Justin Best regards, Mijiddorj - Message: 1 Date: Fri, 17 Apr 2020 11:51:25 -0400 From: Justin Lemkul To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Failed to find GROMACS magic number in trr frame header Messa

Re: [gmx-users] Segmentation fault (core dumped) error during minimization

On 4/19/20 2:43 PM, Elham Taghikhani wrote: Hi  I am simulating a protein-ligand system, using oplss force field but i got this error during minimization. Steepest Descents:    Tolerance (Fmax)   =  1.0e+03    Number of steps    =    5 Step=    0, Dmax= 1.0e-02 nm, Epot=  1.2715

Re: [gmx-users] about correct methodology to run MD of small molecule in gromacs

On 4/18/20 7:39 PM, lazaro monteserin wrote: Dear Gromacs users, As I have referred before I am simulating small molecules (nucleosides) (around 33 atoms) in vacuum in Gromacs. When I do the simulations at the end I want to select the most stable structure from the trajectory for the next ste

Re: [gmx-users] Regarding use of harmonic wall model

On 4/18/20 4:43 AM, Shashank Ranjan Srivastava wrote: Hello everyone, I want to create a gap between the first and last strand of a beta barrel so that I can put a new strand in between. So, I have generated an input file using charmm-gui and using its gromacs production file (production.mdp)

Re: [gmx-users] Residue ‘XXX’ not found in residue topology database - SnCl6

On 4/17/20 5:25 PM, Paolo Costa wrote: Hi Justin, thanks a lot. I tried as you said and I changed from SnCl6 to SnC in my stannate.pdb and also to stannate.rtp. But still I get the error. Here the output file of from pdb2gmx: Opening force field file /usr/share/gromacs/top/amber99.ff/aminoac

Re: [gmx-users] Residue ‘XXX’ not found in residue topology database - SnCl6

On Fri, Apr 17, 2020 at 4:50 PM Paolo Costa wrote: > Dear GROMACS user, > > I am aware that such error occurs frequently for new users as I am. > I am learning how to add new residue in Gromacs; I tried first following a > tutorial ( > https://www.svedruziclab.com/tutorials/gromacs/2-methane-in-w

Re: [gmx-users] Failed to find GROMACS magic number in trr frame header

On 4/17/20 10:13 AM, Mijiddorj B wrote: Dear GMX users, Hello, I performed MD simulation using gromacs 2018.7v. During this simulation, the calculation was stopped because of the electric cut. Then, I continued the simulation using "gmx mdrun with -noappend" in order to get separate trajector

Re: [gmx-users] Dramatic decrease NVE production

On 4/17/20 10:31 AM, Dorj Bat wrote: Dear users, I would like to perform MD simulations using NVE simulation and to check temperature increasing behavior while applying an E-field. However, I started a short 100 ps simulation. Initial velocity was generated around T=300K. However, the syste

Re: [gmx-users] Does the energy minimization deals with velocity ?

On 4/17/20 11:06 AM, Mohamed Abdelaal wrote: Hello everyone, If I will add the velocity manually to my system, should I add them before the energy minimization or after ? I will do the below steps: 1. insert molecules 2. energy minimization 3. NVT equilibiration 4. NPT equilibiration 5. prod

Re: [gmx-users] Measuring bond distances, angles and dihedrals

On 4/17/20 9:19 AM, Smith, Micholas D. wrote: Gmx chi I believe gives the dihedral information. Distances can be obtained from gmx mindist More generally, gmx angle or gangle are for angles and dihedrals (and gangle can calculate angles between planes and/or vectors as may be required her

Re: [gmx-users] weird output from simultions of a protein between two sheets

uction run. I do block averages. I have saved the data every step because I tried to trace the problem. Greetings Zuzana - Original Message ----- From: "Justin Lemkul" To: "gmx-users" Sent: Friday, April 17, 2020 1:48:28 PM Subject: Re: [gmx-users] weird outpu

Re: [gmx-users] weird output from simultions of a protein between two sheets

On 4/17/20 7:14 AM, Zuzana Benkova wrote: Dear Gromacs users, I want to simulate a protein between two graphene sheets separated by 21 nm. The system is solvated and placed in the cell of dimensions 17.09360 17.18200 25.0. The energy minimzation of this system with position restrain a

Re: [gmx-users] position restrain of water

On 4/17/20 7:42 AM, m g wrote: Dear All, I want to restrain just my drug in product step in all of the simulation time. Hence, I used #define = -DPOSRES in the product.mdp file.In my topol.top file there is below lines: ; Include water topology#include "oplsaa.ff/spce.itp" #ifdef POSRES_WATER

Re: [gmx-users] atomtype "OE" in charmm36

On 4/17/20 4:45 AM, Schirra, Simone wrote: Dear Gromacs users, I want to simulate polyethylene glycol and I am using a script to build my .itp and .gro files. The script is designed to work with charmm35r, however I only found charmm36 available now (I read, that c35r was only temporary). I

Re: [gmx-users] ' LONEPAIR LP1 ' gives error message in protein - ligand simulation

On 4/17/20 12:15 AM, Adarsh V. K. wrote: Dear all, A ligand molecule (lig) contains a Chlorine atom in it. While attempting to performing a protein-ligand simulation, the Gromacs returns an error message. It is observed that the *CGenFF server * Generate two additional lines, as shown below,

Re: [gmx-users] Question on running gmx trjconv without 2 prompts

On 4/16/20 8:12 PM, Lei Qian wrote: Dear users, Could I ask: how to run gmx trjconv without 2 prompts? I select 'Protein' to center, and 'System' to output. I put indexes of 'Protein' and 'System' into 1 .ndx file, add -n Protein_System.ndx to gmx trjconv command, however, Gromacs cannot do

Re: [gmx-users] about problem running script for Gibbs free energy simulation

On 4/16/20 3:20 PM, lazaro monteserin wrote: But how do I declare this in the script? I have try for example: FREE_ENERGY="/home/Lazaro/tutorial_gromacs" and then MPD="/$FREE_ENERGY/mpd" Using the " " But stills it doesn't work. I have all my .mdp files stored in a directory called "mdp" i

Re: [gmx-users] about problem running script for Gibbs free energy simulation

On 4/16/20 1:47 PM, lazaro monteserin wrote: Dear Lemkul Thank you very much for the recommendation. I tried each step but separate and you were right I was missing the .gro in my directory. Now the script should work. But I am still unsure of how to declare the location of my file in the e

Re: [gmx-users] about problem running script for Gibbs free energy simulation

On 4/16/20 11:48 AM, lazaro monteserin wrote: Dear Gromacs users, I have been trying to do the tutorial title: "Free Energy Calculations: Methane in Water" by Dr. Justin A. Lemkul but when I try to actualize my paths to the variables $FREE_ENERGY AND $MDP in the script *job.sh* I have problem

Re: [gmx-users] WARNING 1 [file topol.top, line 60334] - How to manage? -maxwarn 1 or any other solution

On 4/16/20 10:26 AM, Adarsh V. K. wrote: Dear all, While performing a protein ligand simulation, I received the following 'WARNING' message. How to manage this issue? just with ' -maxwarn 1 ' or any other method? ---

Re: [gmx-users] semiisotropic pressure coupling.

On 4/14/20 10:12 PM, Miro Astore wrote: Hello all, I am working with a rather large membrane bound protein. I was getting an issue awhile ago where if the protein moved to the edge of the box the box would elongate in the z direction. I fixed this in the short term by setting my xy compressib

Re: [gmx-users] How to prevent velocity generation for my position restrained molecules ?

On 4/14/20 5:48 PM, Mohamed Abdelaal wrote: Hello everybody, I am simulating the evaporation process for different atoms on a graphene sheet and the z-coordinate of each graphene carbon atom was restrained (using position restrain). The energy minimization was successfully done without any e

Re: [gmx-users] Velocities from the .gro file

On 4/14/20 4:55 PM, Mohamed Abdelaal wrote: Sorry for writing again in the same topic but I couldn't solve the velocity problem. I am trying to reproduce a paper written by: Claire Tonnel + , Martin Stroet + , Bertrand Caron, Andrew J. Clulow, Ravi C. R. Nagiri, Alpeshkumar K. Malde, Paul L. B

Re: [gmx-users] Basic question about command line

On 4/13/20 10:03 PM, Mohammad Madani wrote: Dear all Hi, I have a basic question about the using the gromacs. I want to use gmx cluster for clustering. I use the cluster hpc. When I run the this command: gmx cluster -f *.trr -s *.gro -g *.log -clid *.xvg I receive the error that I should selec

Re: [gmx-users] how to run equilibration when freezing part of an small molecule in vacuum and in water environment?

On 4/13/20 10:37 AM, lazaro monteserin wrote: Dear Gromacs users I have three questions about the details of running MD of small molecules in gromacs: 1) If I run a MD in vacuum if I freeze part of the nucleoside (lets say the carbons in the sugar) with genrestr, should I use temperature cou

Re: [gmx-users] Problem with pdb2gmx

On 4/12/20 2:42 PM, Elham Taghikhani wrote: Hi Yes the spacbond.dat and residuetypes.dat files are in my oplsa folder in my working directory. These files should be in the working directory, not in the force field subdirectory. This is why they are not being read. When it gives me topol.

Re: [gmx-users] duplicate angle index- angle restraint

On 4/12/20 7:40 AM, Sadaf Rani wrote: Dear Justin As per table 5.14 in manual, For angle restraints it selects [image: image.png] Also in manual under heading *Angle restraints*, it is mentioned that these are used to restrain the angle between two pairs of particles or between one pair of p

Re: [gmx-users] duplicate angle index- angle restraint

On 4/12/20 7:12 AM, Sadaf Rani wrote: Dear Gromacs users I am putting some restraints on bonds angles and dihedrals during free energy calculations for which the topology file section is as below:- ; distance restraints [ bonds ] ;i j type r0A r1A r2AfcAr0B r1

Re: [gmx-users] Problem with pdb2gmx

On 4/11/20 2:55 PM, Elham Taghikhani wrote: Thank you. I did what you said and added new bond to specbond.dat file like this: 10 LYS CD  2   FLO NZ  2   1.8 LYS    FLO LYS NZ  2   FLO CX  2   1.8 LYS     FLOCYS    SG     1    CYS    SG  

Re: [gmx-users] Problem with pdb2gmx

On 4/11/20 12:16 PM, Elham Taghikhani wrote: Thank you for your suggestion. I gave the molecule new chain identifier and they are HETATOM in my pdb file.but still it has this warning: Warning: No residues in chain starting at FLO1 identified as Protein/RNA/DNA. This makes it impossible to l

Re: [gmx-users] Problem with pdb2gmx

On 4/11/20 5:38 AM, Elham Taghikhani wrote: Hi Thank you for your response. I added my ligand pdb file to the protein pdb file, then the ligand name as a protein/other (tried both) to the residuetype.dat file , but still it has warning in this case. As i said before I modified the rtp file

Re: [gmx-users] Regarding version of gromacs

On 4/10/20 9:20 PM, Ashma Khan wrote: Thank you Justin for your suggestion As I run my simulation on supercomputer and there is availability of gromacs-5.1.2 version not 5.1.4. Earlier it had 5.1.4 version but now it has only 5.1.2 version. You can always install the version you want in you

Re: [gmx-users] pdb2gmx: Selecting Force Field in first command

On 4/10/20 9:03 PM, ferna...@hypernetlabs.io wrote: Hi all! Context I'm trying to run simple gromacs example commands below * gmx pdb2gmx -f 1aki.pdb -o 1aki_processed.gro -water spce * gmx pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc In a Do

Re: [gmx-users] segmentation fault gmx do_dssp

On 4/10/20 8:07 PM, Sadaf Rani wrote: Dear Justin and Qinghua I am using gromacs 2020 for analysis and dssp version on my system is 2.2.1. Which version of dssp would be compatible with gromacs 2020? Your version should be fine, but make sure the dssp binary works properly on its own (not

Re: [gmx-users] How to extend the force field by polariation parameters

Original Message - From: "Justin Lemkul" To: "gmx-users" Sent: Friday, April 10, 2020 3:05:47 PM Subject: Re: [gmx-users] How to extend the force field by polariation parameters On 4/9/20 8:06 PM, Zuzana Benkova wrote: Dear GROMACS users, I am trying to extend the

Re: [gmx-users] segmentation fault gmx do_dssp

On 4/10/20 5:48 PM, Sadaf Rani wrote: Dear Gromacs users I am doing an analysis of protein-ligand MD simulation of 150ns. I am trying to calculate secondary structure as below:- gmx do_dssp -f md_noPBC.xtc -s md.tpr -o ss.xpm -tu ns -dt 1 But I am getting segmentation fault error. Reading fi

Re: [gmx-users] dt in mdp

On 4/10/20 4:17 PM, Alex wrote: On Fri, Apr 10, 2020 at 9:19 AM Justin Lemkul wrote: On 4/10/20 9:16 AM, Alex wrote: Thank you for the response. On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul wrote: On 4/10/20 8:13 AM, Alex wrote: Dear Justin, Any comment please? Sorry, haven'

Re: [gmx-users] Problem with pdb2gmx

On 4/10/20 12:15 PM, Elham Taghikhani wrote: Hi I want to simulate a protein which is bound covalently to a ligand. When I get the gro file of the complex the bond between the amino acid and the ligand is broken although I had modified the .rtp file before and it seems ok in a PDB format.

Re: [gmx-users] GROMACS version issue

On 4/10/20 11:04 AM, Yasaman KARAMI wrote: Dear GROMACS developers, I am performing classical MD simulations of a membrane protein system, using GROMACS 2018.6 version. I have just noticed that after few nano seconds, the box dimensions are changing. Meaning that the system shrinks along t

Re: [gmx-users] Regarding version of gromacs

On 4/10/20 9:21 AM, FAISAL NABI wrote: I have tried the same few days back but it didn't work. I have been using gromacs 2018.1 earlier and then switched to 5.1.4 and it didn't work. Switching between major versions that are years apart in their development will not work, and GROMACS has ne

Re: [gmx-users] dt in mdp

On 4/10/20 9:16 AM, Alex wrote: Thank you for the response. On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul wrote: On 4/10/20 8:13 AM, Alex wrote: Dear Justin, Any comment please? Sorry, haven't had power/network for a while due to some bad storms here. GROMOS force field

Re: [gmx-users] How to extend the force field by polariation parameters

On 4/9/20 8:06 PM, Zuzana Benkova wrote: Dear GROMACS users, I am trying to extend the CHARMM force field of graphene by polarization of carbon atoms. I need to use the rigid rod dipole model, with a dipole on each carbon atom, with length of 0.7 A° combined with a charge of 0.1 e, which yi

Re: [gmx-users] Fwd: geometry optimization of metalloenzyme

and I strongly discourage using it. The crash may be due to failure to use energygrp_exclusions when freezing or due to intrinsic instability of the system that even freezing cannot overcome. -Justin On Thu, Apr 2, 2020 at 9:26 PM Justin Lemkul wrote: On 4/2/20 3:23 PM, Nadia Elghobashi

Re: [gmx-users] dt in mdp

y = 4.5e-5 ref_p= 1.0 refcoord-scaling = com energygrps = thin_film SOL comm-mode= Linear nstcomm = 100 comm-grps= Thin_fiml SOL %- Thank you Alex On Tue, Apr 7, 2020 at 5:0

Re: [gmx-users] dt in mdp

On 4/7/20 5:00 PM, Alex wrote: Dear all, After minimization and equalizations using nvt (v-rescale) and npt (both berendsen and ;Parrinello-Rahman), a simulation of mine could run well for 200 ns using dt =0.001 while it would crash after 3 ns If I used dt = 0.002 with the particles communicat

Re: [gmx-users] restarting a simulation

On 4/7/20 11:47 AM, Daniel Burns wrote: You should also have an "md10.cpt" in addition to the "md10_prev.cpt"? If so, replace it in your command with just the md10.cpt file. If you don't have it, try renaming your "_prev.cpt" file to just "md10.cpt". The issue is not with the naming of the

Re: [gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units

On 4/7/20 10:10 AM, ZHANG Cheng wrote: Dear Andre, Thank you for the advice. Can I ask, 1) Could you please clarify the concepts? I know "constraint" and "restraint" are two different things in gromacs. And "fix" is another term? How about "freezegrps"? I would not use "fix" and "restrain

Re: [gmx-users] Velocities from the .gro file

On 4/6/20 12:16 PM, Mohamed Abdelaal wrote: Hello everybody :) Can I use the gmx insert-molecules to insert molecules in my box with velocities by adding the velocities in the .gro file and insert the molecules from this .gro file ? Have you tried it? -Justin -- ==

Re: [gmx-users] Fumbling in the dark with dihedral pulling

d it personally. -Justin With Regards Marko Petrovic Educator Computational Science and Technology School of Electrical Engineering and Computer Science KTH Royal Institute of Technology On 6 Apr 2020, at 14:44, Justin Lemkul mailto:jalem...@vt.edu>> wrote: On 4/6/20 2:33 AM, Marko Petrov

Re: [gmx-users] Bonds definition in itp files

t the force field applies constraints to all bonds or only bonds to H. If the latter, you shouldn't apply ad hoc constraints. -Justin On Mon, 6 Apr 2020 at 17:12, Justin Lemkul wrote: On 4/6/20 7:24 AM, Sina Omrani wrote: Hi, I wanted to know how we specify a bond order in our simul

Re: [gmx-users] Fumbling in the dark with dihedral pulling

On 4/6/20 2:33 AM, Marko Petrovic wrote: I figure it might be helpful to see my other files so I include a link: https://github.com/SpaceDucK77/StringMethodMaster/tree/master/Prototypes/P3_Pull_coordinates/manual_test_justin Your dihedral definitions are simply incorrect. pull_coord1_group

Re: [gmx-users] Bonds definition in itp files

On 4/6/20 7:24 AM, Sina Omrani wrote: Hi, I wanted to know how we specify a bond order in our simulation? For example, if we have a triple bond in our structure between atoms 1 and 2, is it by length and force constants or we define 1 and 2 bonds three times in the bond section of itp file? Wh

Re: [gmx-users] Protonation state of aminoacids from pdb and pdb2gmx

On 4/6/20 8:10 AM, Javier Luque Di Salvo wrote: Dear Gromacs users, I'm aware that there might be plenty of discussions on this matter, anyway I would like to get your advice. Which is the proper way to know the protonation state that is generated with pdb2gmx? I have downloaded a pdb file fr

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