[gmx-users] grompp warning

Hello GMX users, I added another ligand as a new residue in the topology database, and then build the topology of the liand with pdb2gmx, everything worked well. But I got this warning from grompp for a nvt equilibration after successful minimizations: There are atoms at both ends of an

Re: [gmx-users] Using external force field with GROMACS

Hello, You can also set the variable of GMXLIB so that pdb2gmx can find the force field you want to use, like: GMXLIB=/ path /charmm36m.ff Best, Qinghua On 07/28/2017 10:53 AM, Souparno Adhikary wrote: Hi, I want to use the latest CHARMM36m force field which I downloaded from MacKerell

Re: [gmx-users] Atom OXT in residue was not found

Dear Justin, Thanks very much for your suggestion, it works well now. All the best, Qinghua On 08/09/2017 01:28 PM, Justin Lemkul wrote: On 8/9/17 7:21 AM, Qinghua Liao wrote: Hello, I want to simulate a protein with a ligand (small molecule, 15 atoms). But I have problem of generating

Re: [gmx-users] Lincs constraints failure

? Apart from using smaller time step (i.e. 1 fs), is there some other solution? Thanks a lot! All the best, Qinghua On 06/25/2017 09:04 PM, Mark Abraham wrote: Hi, What are you exchanging between replicas? Seems like the most likely issue. Mark On Sat, 24 Jun 2017 16:50 Qinghua Liao <scorpi

[gmx-users] Lincs constraints failure

Hello, I have searched on Google for the LINCS warning problems, and there are already many discussions, but I guess that my situation might be different. I have a system of protein/micelles/water_ions in a dodecahedral water box. The system is fully equilibrated by several steps. 1.

[gmx-users] mixed 1-4 scaling factor

Hello, I want to simulate a system using Amber and Glycam force fields together with gromacs, I am wondering whether a scheme of mixed 1-4 scaling factors is available with Gromacs. I searched the mailing list, and I found this post which no one responded:

[gmx-users] charmm 36 force field for DNA

Hello, I want to simulate a DNA with CHARMM 36 force field, but I found that the atom names in the pdb downloaded from the PDB data bank do not match those in the CHARMM 36 force field. Is there a better tool to edit it properly than modifying manually? Thanks a lot! PS: They match well with

Re: [gmx-users] set computer time on REMD simulation

Hello, If I understand correctly, it terminates at 0.99*t, t is the time you set in hour. In you case, you simulation should be terminated at 0.1*0.99 = 0.099 h, which is 5.94 minutes. PS: 0.1 h is not 10 minutes, but 6 minutes. All the best, Qinghua On 12/18/2017 08:05 AM, YanhuaOuyang

Re: [gmx-users] How to run MD with longer recording interval to reduce the file size?

Hello, Thank you Justin and Qinghua! Can I ask 1) I could not find "nstfout" (forces) in the md.mdp file from the tutorial. Should I add a new line of "nstfout=0"? Yeah, you can add that line, or you can leave it be, the default is set as ZERO. 2) should I change "nstxout-compressed=5000" to

Re: [gmx-users] How to run MD with longer recording interval to reduce the file size?

Hello, Here is the settings I used in the mdp file, you may consider it. nstxout = 0 ; save coordinates every 2 ps nstvout = 0 ; save velocities every 2 ps nstxtcout   = 500   ; xtc compressed trajectory output every 2 ps nstenergy   =

Re: [gmx-users] How to run MD with longer recording interval to reduce the file size?

Hello, Normally, you don't need to write out the force and velocity, then you can set nstfout and nstvout as ZERO, then only the coordinates will be written out in a xtc file. If you don't care about waters, then you can also set xtc-grps as a group without waters and counterions. Best,

Re: [gmx-users] How to add distance and angle restraints in the topology file?

Hello, I guess you should add your ligand.itp to aminoacids.rtp, and then use pdb2gmx to generate a combined topology file. After that, you can use distance or angle restraints between the protein and the ligand. Maybe you can try to parmed from Amber to combine your protein and ligand

Re: [gmx-users] REMD implicit solvent

Hello, From my experience, the domain decomposition is not compatible with implicit solvent, you have to switch to particle decomposition for the simulations. All the best, Qinghua On 01/05/2018 12:40 PM, Urszula Uciechowska wrote: Hi, I just run a normal single-replica. Now the error

Re: [gmx-users] Catenation error

Hello, I guess that the difference might come from different number of waters, you can first strip all waters from the trajectory files, and then combine them all into one single trajectory file. All the best, Qinghua On 01/05/2018 01:04 PM, suniba wrote: Hello experts and users I have

Re: [gmx-users] Gromacs 2018 installation failed

from here https://www.gnu.org/software/binutils/ and compile it on your own, setting the PREFIX to a directory in your home, then use $PATH to make your binary the highest priority. Cheers, Elton On Fri, Feb 9, 2018 at 8:17 PM, Qinghua Liao <scorpio.l...@gmail.com> wrote: Hello Elton,

Re: [gmx-users] Gromacs 2018 installation failed

, Qinghua Liao <scorpio.l...@gmail.com> wrote: Dear GMX developers, I am trying to install Gromacs2018 with cuda on clusters, the installation was successful on one cluster, but failed on the other cluster. I guess there might be some library missing on the other cluster. For the succeed

[gmx-users] Gromacs 2018 installation failed

Dear GMX developers, I am trying to install Gromacs2018 with cuda on clusters, the installation was successful on one cluster, but failed on the other cluster. I guess there might be some library missing on the other cluster. For the succeeded one, the operating system is openSUSE 42.2

Re: [gmx-users] Why "do_dssp" gives one more residue?

Hello, Maybe you have two chains in your system, then there should be one for chain separator. Best, Qinghua On 02/21/2018 06:20 PM, ZHANG Cheng wrote: Dear Gromacs, My protein only has 442 residues. After running gmx do_dssp -f md_0_1_noPBC.xtc -s md_0_1.tpr -ssdump ssdump.dat -map

Re: [gmx-users] Extending MD simulations

Hello, Normally, what I do is renaming new.tpr as md_0_1.tpr, and run gmx mdrun_mpi -deffnm md_0_1 -cpi md_0_1.cpt -append I will then get appended files. All the best, Qinghua On 12/28/2017 01:20 PM, Pandya, Akash wrote: Hi all, I tried extending my MD simulation from 60 ns to 100 ns

Re: [gmx-users] Trying to use AMBER parameters in GROMACS

Hello, You could try to build the system with AmberTools (it is free), choose the force fields available in Amber. Once you get the topology and coordinates files (prmtop and inpcrd), you can convert them into top and gro in Gromacs format with *parmed*. Then you can perform the simulations

[gmx-users] Fwd: different vectors from gmx covar and gmx anaeig

+0200 From: Qinghua Liao To: gromacs.org_gmx-users@maillist.sys.kth.se Hello, I am doing PCA analysis to characterize the motion of a domain, I got the files: average.pdb eigenval.xvg eigenvec.trr covar.log Then, with "gmx trjconv -f eigenvec.trr -s average.pdb -o eigenvec.pdb&quo

[gmx-users] different vectors from gmx covar and gmx anaeig

Hello, I am doing PCA analysis to characterize the motion of a domain, I got the files: average.pdb eigenval.xvg eigenvec.trr covar.log Then, with "gmx trjconv -f eigenvec.trr -s average.pdb -o eigenvec.pdb", I got all the vectors in the pdb file "eigenvec.pdb" I also used "gmx anaeig -v

Re: [gmx-users] conversion from amber (prmtop and inpcrd) to gromacs itp and gro

Hello, You can also do it with parmed from Amber, here are the python commands: import parmed as pmd #convert prmtop and inpcrd into top and gro amber = pmd.load_file('1N55_apo.prmtop','1N55_apo.inpcrd') # amber.save('topol.top') amber.save('ions.gro') # On 11/7/18 10:07 AM, Rahma Dahmani

Re: [gmx-users] ParmED

Hello, Here is my script " input.py ": # import parmed as pmd #convert prmtop and inpcrd into top and gro amber = pmd.load_file('mol_HMR.prmtop','mol_HMR.inpcrd') # amber.save('topol.top') amber.save('ions.gro') # system = pmd.load_file('topol.top') system.write('topol2.top', combine=[[0,1]]) #

Re: [gmx-users] dssp error

, version 2016.3 Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668) Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. Em qui, 21 de mar de 2019 às 15:53, Qinghua Liao escreveu: Hello, Just follow the suggestion by adding "-ver 2" to yo

Re: [gmx-users] dssp error

Hello, Just follow the suggestion by adding "-ver 2" to your command. All the best, Qinghua On 3/21/19 7:50 PM, Mario Andres Rodriguez Pineda wrote: Good afternoon. I'm using Gromacs 2016 to do a dynamic simulation. I installed DSSP 2.0.4 for secondary structure analysis. When i try to run

Re: [gmx-users] How to calculate distance using gromacs?

Hello, You can do it with gmx mindist, but first you need to make two index group of the two residues. All the best, Qinghua On 2/15/19 2:16 PM, Edjan Silva wrote: Dear, I performed a 100 ns simulation with B-DNA. I want to know which gromacs option I can calculate the distance between

Re: [gmx-users] Hamiltonian replica exchange

Hello Hind, There HREMD is available for Gromacs patched with PLUMED, and there is a tutorial you can go through: https://www.plumed.org/doc-v2.5/user-doc/html/hrex.html All the best, Qinghua On 1/18/20 8:12 PM, hind ahmed wrote: Dear, is there a tutorial to run Hamiltonian replica

Re: [gmx-users] Restarting a REST2 simulation

Hello Joseph, You can have a check all the cpt files, to see whether they were all saved at the same simulation time. Sometimes, some of the cpt files can be incomplete when saved at the last second. All the best, Qinghua On 4/9/20 11:23 AM, Joseph, Benjamin Philipp wrote: Dear members of

Re: [gmx-users] segmentation fault gmx do_dssp

Hello, I guess the problem is about memory. You could strip the water and ions first, then process the striped trajectory. All the best, Qinghua On 4/10/20 11:48 PM, Sadaf Rani wrote: Dear Gromacs users I am doing an analysis of protein-ligand MD simulation of 150ns. I am trying to

Re: [gmx-users] Concatenating trajectories

Hello, There is an option of -settime for gmx trjcat, with which you can set different starting simulation time for each trajectory. All the best, Qinghua On 4/9/20 1:26 PM, Pandya, Akash wrote: Hi, I have four trajectories of the same condition (protein only) that I want to concatenate.