[gmx-users] slurm and gromacs

Dear gromacs users I am doing md simulation of protein in a cluster system with Slurm Workload Manager using following job file: --- #! /bin/bash #SBATCH --job-name Pr_lig #SBATCH -n 28 #SBATCH --time 300:30:00 #SBATCH --mem

[gmx-users] grompp error : Atomtype CAro not found

Dear Justin and Dallas, Thanks for your answers. I am so confused. I am beginner in MD simulation of lipid + small molecule. '' There are far better options for lipids than the old Berger parameters used in the tutorial. I wrote the tutorial in 2008 and it reflected a common protocol at the time

[gmx-users] grompp error : Atomtype CAro not found

Hi Dallas, thanks for your answer. I saw README file in gromos54a7_atb.ff from ATB server. My system contains lipid molecules and small molecule. For lipid molecules, Justine Lemkul suggested to use gromos53a6_lipid.ff. How to use both of gromos54a7_atb.ff and gromos53a6_lipid.ff in topology

[gmx-users] grompp error : Atomtype CAro not found

Hi gromacs users, I am doing MD simulation of my system (DPPC lipid + 2 drug molecules + water molecules) using gromacs 2019. I used ATB for drug molecules and Membrane Protein: KALP15 in DPPC gromacs tutorial method for lipid molecules (based on Justin Lemkul suggestion in my previous post:

[gmx-users] grompp error : Atomtype HC not found

Dear Justin, Thanks for answer. You said " There is no reason to use this totally obsolete force field (ffgmx.itp)". I used ffgmx.itp, because there was a example.top file in Tieleman's web site: --- ; topology for 1 alm molecule, 128 popc

[gmx-users] grompp error : Atomtype HC not found

Hi gromacs users, I am doing MD simulation of my system (DPPC lipid + 2 drug molecules + water molecules) using gromacs 2019. I used ATB for drug molecules and Tieleman's web site for lipid molecules. --- My topology file is as follows:

[gmx-users] topology files for lipid bilayer

Dear gromacs users, I want to do MD simulation of the lipid bilayer-ligand system. I used MD topology file from Automated Topology Builder (ATB). ATB got GROMACS G54A7FF United-Atom (ITP file) for ligand molecule. How to get appropriate topology files for lipid bilayer? Please guide me about

[gmx-users] g_mmpbsa for rna-rna complex

Hi gromacs users, I want to do md simulation of rna-rna complex. Can I do g_mmpbsa tools for calculation of Delta G binding? Best, Atila -- 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

[gmx-users] mdrun stopped without error

Hi all, I am doing md simulation. But mdrun stopped without any error in log file. I repeated it. But mdrun stopped again in another step. What is the reason of stopping. Best, Atila -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Inconsistency in user input:

With gmx_mpi mdrun -v -deffnm nvt_pr, there is not error. -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit

[gmx-users] Inconsistency in user input:

Dear gromacs users, I am doing md simulation (nvt equilibration step) using gromacs version 2018.2. After using (gmx_mpi mdrun -v -deffnm nvt_pr -nb gpu), I encountered with: Program: gmx mdrun, version 2018.2 Source file: src/gromacs/taskassignment/decidegpuusage.cpp (line 292) Function:

[gmx-users] unusual trajectory

Dear Alex and gromacs users, I used trjconv -pbc whole. But my problem was not solved. You said "What I am trying to say is that per se nothing wrong seems to be happening". As I uderstood, in analyses such as gmx rms and gmx distanc and gmx traj (which I need them) this trajectory is not

[gmx-users] unusual trajectory

Dear Alex, Thanks for answer. "What I am trying to say is that per se nothing wrong seems to be happening" Based on your answer in previous post, can I use this trajectory for analysis? Best, Atila -- Gromacs Users mailing list * Please search the archive at

[gmx-users] unusual trajectory

Dear Alex, Which group I should select (system, CNT or lig)? After selecting each of them: There were 44 inconsistent shifts. Check your topology I'm confused. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] unusual trajectory

Dear gromacs users, After doing NVT md simulation of CNT + LIG + WATER molecules, I encountered with unusual structure of LIG molecule in some frames in trajectory viewing using VMD. https://1drv.ms/u/s!AveJH4Y30cH0sQu08knJYk7TGc7g My mdp file for this md is as follows: define =

[gmx-users] CNT md simulation & unusual Equilibrated structure (NVT)

Hi all, Excuse me for my questions. After energy minimization, I did NVT equilibration phase. Unfortunately, I did not find an appropriate tutorial and mdp file for CNT simulation. I used following mdp file: integrator = md nsteps = 5 dt = 0.002 energygrps = CNT LIG nstxout = 500

[gmx-users] CNT md simulation & unusual minimized structure

Dear Justin, Thanks for your answer. I rechecked box dimension (along Z) and corrected it. My problem was solved. Best, Atila -- 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

[gmx-users] CNT md simulation & unusual minimized structure

Dear gromacs users, I am doing md simulation of cnt + drug (lig) + water molecules. I get lig.gro and lig.itp files using antechamber module and amb2gmx script. I used cnt force field parameters from paper (*https://pubs.acs.org/doi/abs/10.1021/jp011344u

[gmx-users] energy minimization_note

Dear Mark, Thanks for your answer. “But typically EM in vacuum is short enough you should not consider optimizing it.”. You are right. Using the reference manual about PME, I created new mdp file as follows: integrator = steep nsteps = 5 emtol

[gmx-users] energy minimization_note

Dear gromacs users, I am doing md simulation of cnt + drug + water molecules. The em.mdp file is follows: integrator = steep nsteps = 5 emtol= 10 emstep = 0.01 ns_type = grid rlist =

[gmx-users] x2top_error

Hi gromacs users, I used following command for CNT. gmx_mpi x2top –f cnt.gro –o cnt.top –ff cnt –name CNT –pbc -noparam I encountered with: . . . . . . Can not find forcefield for atom CA-968 with 5 bonds Can not find forcefield for atom CA-970 with 5 bonds Can not find forcefield

[gmx-users] trjcat -settime

Dear Justin, I used following: continuation = no, in nvt.mdp (first md run, 500 ps) continuation = yes, in npt.mdp (second md run, 1000 ps). Is my manner wrong? -- Gromacs Users mailing list * Please search the archive at

[gmx-users] trjcat -settime

Hi Justin, Thanks for answer. I used trjcat again but with following. File Current start (ps) New start (ps) - nvt.trr0.000 ps 0 npt.trr0.000 ps

[gmx-users] trjcat -settime

Dear gromacs users, I did 2 md simulations: first 500 ps (a.trr) and second 1000 ps (b.trr). I want to join these trajectories. I used following command: gmx trjconv -f a.trr b.trr -o all.trr -settime Summary of files and start times used: File Current start (ps)

[gmx-users] md simulation of oil hydrocarbon / L-OPLS

Dear Micholas, I have many hydrocarbons (small to large) for study, C8 - C50, . -- 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 http://www.gromacs.org/Support/Mailing_Lists * For

[gmx-users] md simulation of oil hydrocarbon / L-OPLS

I know your mean. But there is not octane residue type in rtp file. -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe

[gmx-users] md simulation of oil hydrocarbon / L-OPLS

I did what was in README for octane molecule, but: Fatal error: Residue 'LIG' not found in residue topology 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

[gmx-users] md simulation of oil hydrocarbon / L-OPLS

Dear Justin, I found L-OPLS in GitHub: https://github.com/wesbarnett/lopls Can I use it directly for hydrocarbon such as octane? -- 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

[gmx-users] md simulation of oil hydrocarbon / L-OPLS

Hi, I found a paper entitled " Optimization of the OPLS-AA Force Field for Long Hydrocarbons " (https://pubs.acs.org/doi/abs/10.1021/ct200908r). They obtained L-OPLS force field. Which version of gromacs has L-OPLS force field? -- Gromacs Users mailing list * Please search the archive at

[gmx-users] md simulation of oil hydrocarbon

Hi all, I want to do md simulation of oil hydrocarbon? Is there appropriate force field for these hydrocarbons in gromacs? What I see in gromacs force fields only was related to aminoacids and nucleotides. What is your suggestion for md simulation of oil hydrocarbon? Best, -- Gromacs Users

[gmx-users] velocity

Dear Mark and Justin, My problem was solved using trr file. Thanks for guidance. -- 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 http://www.gromacs.org/Support/Mailing_Lists * For

[gmx-users] velocity

Dear Justin, In my last md simulation, I used nstxout = 1000 nstvout = 1000 nstxtcout = 1000 nstenergy = 1000 nstlog = 1000 After your suggestion, I used gmx traj -f npt.xtc -s npt.tpr -ov veloc.xvg -n index.ndx veloc.xvg file is as follows:

[gmx-users] velocity

Dear Mark, Thanks for your answer. "Only if you asked for velocity information to be written to the trajectory, with nstvout" Usually, I use the following lines in mdp files: nstxout = 1000 nstvout = 1000 nstxtcout = 1000 nstenergy = 1000 nstlog = 1000 But, I get only position of atoms

[gmx-users] md simulation of oil hydrocarbon?

Hi all, I want to do md simulation of oil hydrocarbon? Is there appropriate force field for these hydrocarbons in gromacs? Is it possible with gromacs? Best, -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] velocity

Dear gromacs users, I did md simulation. I need to velocity values for each atoms in time steps. Can I get this parameter from trajectory file directly? How to obtain that? Thanks -- Gromacs Users mailing list * Please search the archive at

[gmx-users] md simulation of a protein in mixture of water and DMSO

Dear gromacs users, I want to do md simulation of a protein in mixture of water and DMSO molecules. Is it possible with gromacs? How to do it? How to obtain itp file for DMSO? Any help will highly been appreciated. Best, Atila -- Gromacs Users mailing list * Please search the archive at

[gmx-users] md simulation of circular rna

Dear all, Can I do md simulation of circular rna using gromacs? Best regards, Atila -- 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 http://www.gromacs.org/Support/Mailing_Lists * For

[gmx-users] concatenate 2 trajectory files

Dear gromacs users, I had done a md simulation for 100 ns. I continued that for another 50 ns. gmx grompp -f 100.mdp -c eq.gro -p system.top -o 100.tpr -n index.ndx gmx mdrun -nb gpu -v -deffnm 100 gmx grompp -f 50.mdp -c 100.gro -p system.top -o 50.tpr -n index.ndx gmx mdrun -nb gpu -v -deffnm

[gmx-users] xtc trajectory only

Dear Mark, Thanks for your answer. I deleted (nstxout = 5000) in mdp file. But still both of xtc and trr trajectory files were created. Best, Atila -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

[gmx-users] xtc trajectory only

Dear Gromacs users, I am using the following mdp options: integrator = md dt = 0.03 nsteps = 500 nstcomm = 100 nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog

[gmx-users] 1-4 VDW and 1-4 EEL Energy Components in mm-gbsa

Dear Amber users, I did mm-gbsa calculation for my protein-ligand complex. Differences (Complex - Receptor - Ligand): Energy ComponentAverage Std. Dev. Std. Err. of Mean --- BOND

[gmx-users] CG run on GPU

Dear gromacs users, Can I do Coarse-grained simulation on GPU? Is there a tutorial for that? Best, AP -- 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

[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

Dear Justin, Thanks for your answers and helps. My mdrun was finished. > If you want specific help about why you're observing some given > speed/performance, you need to provide actual details about the simulated > system, hardware, etc. and upload full .log files to a file-sharing service >

[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

Dear Justin, Thanks for your good guidance (There is only one program now.). My previous problem was solved. Now, I have another question. I used two times following commands for my system (protein): gmx_mpi mdrun -v -deffnm npt >& npt_1.job & gmx_mpi mdrun -nb gpu -v -deffnm npt >&

[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

Dear Mark, In /usr/local/gromasc/bin directory, there are only demux.pl gmx-completion.bash gmx-completion-gmx_mpi.bash gmx_mpi GMXRC GMXRC.bash GMXRC.csh GMXRC.zshxplor2gmx.pl In this directory, there is gmx_mpi rather than gmx. It is true based on the

[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

Dear Mark, > you still need to source the GMXRC from the version you want to use > > in > the terminal you want to use it from. I used source /usr/local/gromacs/bin/GMXRC, But, when I use gmx pdb2gmx command, I encountered with: -bash: gmx: command not found Best, Atila -- Gromacs Users

[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

Dear Justin, Thanks for your answer. I know several programs have been renamed in new version such as pdb2gmx --> gmx pdb2gmx. But when I use gmx pdb2gmx, -bash: gmx: command not found Best, -- Gromacs Users mailing list * Please search the archive at

[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

Dear Mark, Thanks for your quick answer. Now, how to use gromacs 5.1.3 commands? The reason of my question: There is gromacs 4.5.4 (in /opt/bio directory) in my Rocks cluster system by default. I used source /usr/local/gromacs/bin/GMXRC, then pdb2gmx Unfortunately, pdb2gmx related to

[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

Dear Mark, Thanks for the guidance. I updated gcc using your proposed link (https://ed.braaten.net/blog/ 2014-05-28-devtools-for-centos/). Now my Rocks cluster system has following info: Rocks 6.2 CentOS 6.6 Cuda 7.5 and 8 (/usr/local/cuda) gcc 4.8.2 I installed gromacs 5.1.3 based on

[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

Dear gromacs users, I am using Rocks cluster system with following info: Rocks 6.2 CentOS 6.6 Cuda 7.5 and 8 gcc 4.4.7 I am installing gromacs-5.1.3. I used following command: cmake .. -DGMX_BUILD_OWN_FFTW=OFF -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=ON -DGMX_GPU=ON But I encountered with

[gmx-users] Gromacs installation on GPU

*Dear* *Szilárd, * *Thanks for your answer,* > There's the issue. You need to tell the build > system where CUDA is, e.g. by setting the > CUDA_TOOLKIT_ROOT_DIR environment variable. *How? Which command is required in linux?* *Best, * *Atila* -- Gromacs Users mailing list * Please search

[gmx-users] Gromacs installation on GPU

Dear gromacs users, I am installing gromacs in my system. My computational system is Rocks 6.1.1. I encountered with following: [root@me build]# cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON -DGMX_GPU=ON -- The C compiler identification is GNU 4.4.7 -- The CXX compiler identification is GNU

[gmx-users] Wrote pdb files with previous and current coordinates step 0Segmentation fault

Dear Gromacs users, I am doing Tutorial being in the following address by Gromacs 5.0.5 (MD simulation of Protein with CG force field): http://md.chem.rug.nl/index.php/tutorials-general-introduction/proteins In equilibration step, I encountered with the following error: starting mdrun 'Martini

[gmx-users] charge of aminoacids in an special pH

Dear Gromacs users, I want to study MD simulation of my protein in an special pH (2). I want to investigate partially unfolding in this protein. How to set charge of aminoacids in pdb file, prior to start MD? Any help will highly appreciated. Best -- Gromacs Users mailing list * Please

[gmx-users] installation of gromacs as parallel in a system without access to root

Dear Mark, Thanks for your quick answer. In this case, after using your suggested command: cmake .. -DGMX_GPU=ON -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/marydoe/programs Should I use following commands? make check make install source /home/marydoe/programs/gromacs/bin/GMXRC Are these

[gmx-users] installation of gromacs as parallel in a system without access to root

Dear Gromacs users, I want to install gromacs as parallel in a system without access to root, in a place other than /usr/local. My system is Rocks 6.2 with 3.4.1 version of cmake. I created a directory (installation) to install gromacs there and I used following commands: tar xvzf

[gmx-users] how to install and run gromacs on gpu

Dear gromacs users, I want to have gromacs 5.0.5 on the computer system with gpu. What are the prerequisites for this aim? Please guide me how to install and run gromacs on gpu? Best, Atila -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Invalid order for directive atomtypes-

Dear Justin, Thanks for you quick answer, I checked the your suggested link. these new types and their associated parameters must appear before any [moleculetype] directive. In my lig.itp file, [ atomtypes ] appeared before [ moleculetype ] directive. [ atomtypes ] ;name bond_typemass

[gmx-users] Invalid order for directive atomtypes-

Dear gromacs users, My system contains protein and ligand. I get conf.gro and topol.top for protein using pdb2gmx. I used antechamber and acpype for my ligand. I get 2 files: lig.top and lig.gro. Since it should be just 1 topology file, I modified lig.top as lig.itp and included it in topolo.top

Re: [gmx-users] Invalid order for directive atomtypes-

Dear Justin, I confused. In your tutorial (protein-ligand) ( http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html), you used the following lines (in my case, I did like you) ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif *;

[gmx-users] ambconv tool

Dear gromacs users I want to use ambconv tool to convert amber inpcrd and prmtop files to gromacs top and gro files. I downloaded ambconv.tgz. I unzipped and untarred that. But I don't know how to use this tool. Any help will highly appreciated. -- Gromacs Users mailing list * Please search

[gmx-users] question

Dear gromacs users I want to use LIE to obtain binding free energy for my protein-ligand complex. Can I use 0.181 and 0.5 as alpha and beta coefficients for my system? Are 0.181 and 0.5 appropriate for any kind of protein-ligand complex? Any help will highly appreciated. Best, Atila --

[gmx-users] question

Dear Mark, Thanks for your attention, If I want to use PRODRG server and not ATB for my ligand, how to modify charge and charge group number? I am beginner in this acse, please guide about that. Best wishes, Atila -- Gromacs Users mailing list * Please search the archive at

[gmx-users] question

Dear gromacs users I am doing md simulation of protein-ligand using 5.0 version of gromacs. I want to use prodrg server for my ligand. Based on Justin's opinion, the charges should be modified. The structure of my ligand is in a way that I can't use charge of the functional groups being in

[gmx-users] pH

Dear Erik Thanks for your reply, I have another question. By default, Gromacs considers physiological pH value (7), am I right? Based on experimental data, my project should do under the asidic pH (2). You mentioned to pka. Should I use henderson hasselbalch equation? pH = Pka + log

[gmx-users] pH

Dear Justin, Very thanks for your quick answer. Since I don't know, Please introduce me programs and servers to calculate pka values? Best wishes. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

[gmx-users] pH

Dear Gromacs users, I read some papers in which MD simulation was done under the pH other than 7. How to do this using gromacs package? Thanks in advance, Atila -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] check point file

Dear gromacs users I have a general question about cpt file. Is cpt file created every time mdrun is used, automatically? Or should I use an special option to create a cpt file? For example, if the power fails, how to use the cpt file to resume mdrun? Any help will highly appreciated. --

[gmx-users] all in one pc for MD simulation calculations

Dear gromacs users I have a question about computer which is needed for MD simulation by gromacs. Is an all in one pc appropriate for MD simulation? Any help will highly appreciated. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Invalid order for directive bondtypes

Dear Mark Very thanks for you reply. I solved previous problem by swapping the order of my #include statements in forcefield.itp file. I used grompp for energy minimization, I obtained em.tpr file without any problem. Then I used mdrun for energy minimization, this step was done without error,

[gmx-users] Invalid order for directive bondtypes

my em.mdp file is as follows: integrator = steep nsteps = 5 nstcomm = 1 emtol= 10 emstep = 0.01 ns_type = grid rlist= 0.8 coulombtype = cut-off vdwtype

[gmx-users] Invalid order for directive bondtypes

Dear gromacs users I want to do MD simulation of a CNT. I used aromatic carbon from charmm.ff I created a cnt.ff folder containing following files: ffcnt.atp: --- CA12.01100 ;aromatic C - ffcnt.n2t:

[gmx-users] new analysis in gromacs

Dear Mark I got gromacs-4.0.4.tar.gz from gromacs website. I untarred it. I used tools package provided at that site. Then I did following steps: ./configure make make install make links Apparently, installation is ok. I can use all tools of gromacs (pdb2gmx, g_energy, g_rms, ...). But, when I

[gmx-users] new analysis in gromacs

Dear gromacs users I want to use a new code (g_vesicle_density) in gromacs being in this address: http://md.chem.rug.nl/~mara/softa/. There are 2 related files (g_vesicle_density.c and gmx_vesicle_density.c). I did following steps to use this analysis for my system: 1) I copied the files

[gmx-users] radial density profile

Dear gromacs users I would like to compute the radial density profile (1/nm-3) of different parts of a micelle formed with SDS molecules (such as headgroup, alkyl tail and water) relative to the center of mass of the micelle. Is there a direct tool in gromacs to obtain this parameter? If not,

[gmx-users] radial density profile

Dear Justin Thanks for your quick answer. I want to obtain *radial density profile* relative to COM and not radial distribution function (RDF) relative to COM. Are you sure g_rdf -com is appropriate for this aim? Thanks -- Gromacs Users mailing list * Please search the archive at

[gmx-users] PRODRG -cgnr

Dear Justin Thanks for your answer. I want to use GROMOS96 43a1 force field for my protein and PRODRG parameters for my ligand. I want to use leap-frog algorithm for integrator. Based on your opinion, I don't use QM charges. In these conditions, I will use my first way mentioned in my previous

[gmx-users] PRODRG -cgnr

Dear Justin Thanks for your answer. I'm beginner in this regard. I'm not sure . I think that my molecule is comprised almost of existing functional groups. I attached picture of my molecule to this email. please check it. Please help me to do this issue correctly. Thanks for your time and

Re: [gmx-users] PRODRG -cgnr

Dear Justin Unfortunately, now I don't access the file-sharing system. My ligand molecule is in the below link: http://en.wikipedia.org/wiki/Isoniazid Please check it. On Mon, Jul 28, 2014 at 4:53 PM, Atila Petrosian atila.petros...@gmail.com wrote: Dear Justin Thanks for your answer

[gmx-users] PRODRG -cgnr

Dear Justin Thanks for your quick answers. Based on your answers, what should Ido? You have more experience than me in these regards. What is your suggestion about my ligand molecule? -- Gromacs Users mailing list * Please search the archive at

[gmx-users] PRODRG -cgnr

Dear gromacs users I wan to use PRODRG server to do md simulation of my system (drug-protein complex). I know charge and cgnr parameters obtained from PRODRG (for ligand molecule) are not accurate. I know there are 2 ways to solve this problem: 1) If there are special functional groups in my

[gmx-users] question

Dear all I do not like to replace solvent molecules with Na ions randomly. I like to do that based on potential. Which option is needed in the end of following line (.) ? genion -s *.tpr -o *.gro -p *.top -pname Na -pq +1 -np 5 . Best wishes -- Gromacs Users mailing list * Please

[gmx-users] question

Dear Mark Thanks for your reply. Are you sure there's no support in genion for what is my interest? -- 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

[gmx-users] creation coordinate file with special distance between system components

Dear all My system contains protein and ligand. I know if I do MD simulation, distance between protein and ligand will change. I want to have some coordinate files (gro file) such that in each of coordinate files, distance between protein and ligand be a special value. For example, coordination

[gmx-users] g_energy (energygrps)

Dear all I did 20 ns MD simulation on the system with many atoms (containing chain a, b and c of protein). Unfortunately, I forgot to write energygrps (chain a, b and c) in mdp file. My mdrun last long time. Is there any way to obtain new edr file containing chain a, b and c. Any help will

[gmx-users] g_energy (energygrps)

Dear Justin Thanks for your quick reply. I did before: Thus, I should obtain new tpr file from new mdp file with the desired energygrps: grompp -f new.mdp -c *.gro -p *.top -o new.tpr Then, I should use mdrun -s new.tpr -o new.trr -e new.edr -rerun old.trr Are my manner and commands true?

[gmx-users] g_energy (energygrps)

Excuse me In previous post, sentence in line 3 (I did before:) is wrong. -- 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 http://www.gromacs.org/Support/Mailing_Lists * For

[gmx-users] pbc problem

Dear Justin and Tsjerk you said Some tools handle PBC properly, some don't . I want to know exactly which tools of gromacs handle PBC properly. Can I find these tools in manual? I did simulation of a system containing protein and cnt using gromacs 4.5.6. When I see trajectory by VMD, in some

[gmx-users] pbc problem

Dear Gromacs users I did simulation of a system containing protein and cnt using gromacs 4.5.6. When I see trajectory by VMD, in some frames, protein atoms exit one side of box and enter opposite side of box (pbc problem). I know I should use -pbc option of trjconv tool. But I do not know

[gmx-users] pbc problem

Dear kannan Thanks for your reply Are you sure there is not pbc problem in my case. For example, can I do g_dist tool to obtain distance between protein and cnt? Is output for g_dist true and rational? Best wishes -- Gromacs Users mailing list * Please search the archive at

[gmx-users] pbc problem

Daer kannan Thanks for your reply Picture relating to g_dist is in the following link: https://www.dropbox.com/s/c86ubhdguy9ai8b/g_dist.bmp Distance between protein and cnt was increased in during 1000-2500 ps, exactly those frame are unusaul in VMD (in my opinion, pbc problem). Best wishes --

[gmx-users] pbc problem

Dear Justin Thanks for your reply. To obtain modified trajectory and then comparing with original trajectory, I do not know exactly which of none, mol, res, atom, nojump, cluster or whole is appropriate for me. Best wishes -- Gromacs Users mailing list * Please search the archive at

[gmx-users] deformation in cnt

Dear Justin Thanks for your reply. After energy minimization, all carbon atoms are in true position, inside box but again, both ends of cnt were deformed, same problem I had before I add bond length to the length of CNT in z dimension of box. You mentioned possibly poor input geometry . Please

[gmx-users] deformation in cnt

Dear Justin I built CNT by nano tube modeller. Then, I put protein (fragment model with 15 residues) in appropriate distance of CNT manually. I used force field parameters from following paper: J. Phys. Chem. B 2001, 105, 9980-9987. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] enthalpy and entropy using gromacs

Hi gmx users I want to obtain thermodynamic parameters for protein-ligand interaction. I know to obtain free energy and interaction energy by g_lie or g_bar and g_energy, respectively. Now, I want to know how to obtain enthalpy and entropy using gromacs. Which tool? Any help will highly