Re: [gmx-users] Regarding wired RDF of TMAO and Aminoacid

Please show us the plots (upload to a file hosting site and paste the link in your post) or precisely define your results; also explain precisely why the results are unexpected. Also show us your exact commands. Without this we can not help. From: gromacs.org_gm

Re: [gmx-users] Constant Pressure just in z axis

Use semi-isotropic pressure coupling and use a water-type compressibility in the z dimension by a compressibility of 0 in the x/y dimension. That will give you precisely what you are looking for. We've used it before to simulate octane slabs as lipid bilayer mimetics and it work just fine. Gro

[gmx-users] How to recover a corrupted .edr file

Dear users: I recently experienced some corruption in a .xtc and a .edr file. Recovering the .xtc was pretty easy, I use gmx trjconv -b and -e to get the part before the corruption and the part after the corruption, which was itself a small chunk. This presumably works because trjconv actually

[gmx-users] Regarding wired RDF of TMAO and Aminoacid

Hello, I have run an NPT MD simulation of an amino acid with TMAO (as a cosolvent) and water for different concentration (by varying composition of cosolvent: water). I have used Charmm36 FF for TMAO. Now if i am plotting the RDF for Amino acid v/s Water in the presence of different concentrations

Re: [gmx-users] grompp very slow generating .tpr when excluded bonded neighbours is large

Done Mark, thanks. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every proble

[gmx-users] problem of GB simulation

Hello, I am using the following .mdp file for protein BG solvent simulations. However, the job always failed with the following messages: vol -0.00! imb F 22% step 144100, remaining wall clock time: 207 s vol -0.00! imb F 23% step 144200, remaining wall clock time: 207 s vol -0.00! imb F 23%

[gmx-users] Adding TPO and SEP to amber99sb-ildn.ff - question to aminoacids.hdb entry and "[impropers]" entry in aminoacids.rtp

Hi, I try to add the two AA SEP and TPO to the AMBER99SB-ILDN FF in GROMACS 2016.3. following the instructions on http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field I added TPO and SEP to aminoacids.rtp like: [ TPO ] ; Phosphothreonine from http://personalpages.manche

[gmx-users] WG: Adding TPO and SEP to amber99sb-ildn.ff - question to aminoacids.hdb entry and "[impropers]" entry in aminoacids.rtp

Hi, I try to add the two AA SEP and TPO to the AMBER99SB-ILDN FF in GROMACS 2016.3. following the instructions on http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field I added TPO and SEP to aminoacids.rtp like: [ TPO ] ; Phosphothreonine from http://personalpages.manc

Re: [gmx-users] continue simulation from intermediate frame instead of last frame

Hi, Depends which one... some of them extend the ensemble. Mark On Wed, Oct 4, 2017 at 5:36 PM Myunggi Yi wrote: > Peter, > > (ignoring full precision) Are the thermostat and barostat computed by > coordinates and velocities, in principle ? > > > Myunggi Yi (이명기, Ph. D.), Professor > > Depart

Re: [gmx-users] continue simulation from intermediate frame instead of last frame

Peter, (ignoring full precision) Are the thermostat and barostat computed by coordinates and velocities, in principle ? Myunggi Yi (이명기, Ph. D.), Professor Department of Biomedical Engineering (의공학과 bme.pknu.ac.kr), College of Engineering Interdisciplinary Program of Biomedical Mechanical & El

Re: [gmx-users] continue simulation from intermediate frame instead of last frame

Peter, I see. Thank you for the correction. MY -- 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 https://m

[gmx-users] Constant Pressure just in z axis

Dear users, I would like to keep the pressure (1 bar) in the z direction and there is not any similar condition in X/Y directions, I mean it's not obligatory for keeping the pressure in a specific value in X/Y direction. Is the semiisotropic coupling sufficient to my purpose? If it is, which value

[gmx-users] gmx gpu error gmx: error libnvidia-ml.so.1

Hi all, I tried installing Gromacs 2016.4 on a new hardware with Nvidia Quadro K420 2gb support. Installation completed successfully following Quick and Dirty method. But gmx is not working. Error says: gmx: error while loading shared libraries: libnvidia-ml.so.1: cannot open shared object file

Re: [gmx-users] continue simulation from intermediate frame instead of last frame

Hi MY, actually you lose continuity of your simulation in both cases. The cpt file stores full precision coordinates and velocities (unlike gro/xtc). In addition, it stores state information about the simulation itself, such as the themostat and barostat. Whether this is an issue is up to you of

Re: [gmx-users] continue simulation from intermediate frame instead of last frame

1. In principle, MD can be restarted if there are coordinates and velocities on the snapshot. 2. Even if you don't have velocity, you can assign random velocity with the specific temperature. In this case, you lose continuity of simulation. Don't worry. If you run same simulation with the exactly

Re: [gmx-users] continue simulation from intermediate frame instead of last frame

In that case, I think I do not have any option. The gmx_mpi_d check has only the last frame. :( Command line: gmx_mpi_d check -f ../state.cpt Checking file ../state.cpt # Atoms 10703 Last frame -1 time 190772.080 Item#frames Timestep (ps) Step 1 Time

Re: [gmx-users] continue simulation from intermediate frame instead of last frame

On 10/4/17 9:06 AM, tarak karmakar wrote: Hi Justin, Thanks for the quick reply. Is there any way to check if the frame is there in .cpt file or not? I did the following exercise at difference 'time=' values, gmx_mpi_d convert-tpr -s topol.tpr -f state_prev.cpt -e ener.edr -time 4 -o topo

Re: [gmx-users] continue simulation from intermediate frame instead of last frame

Hi Justin, Thanks for the quick reply. Is there any way to check if the frame is there in .cpt file or not? I did the following exercise at difference 'time=' values, gmx_mpi_d convert-tpr -s topol.tpr -f state_prev.cpt -e ener.edr -time 4 -o topol.tpr It seems in all the cases, the trajecto

Re: [gmx-users] CHARMM2GMX

On 10/4/17 8:36 AM, Sergio Manzetti wrote: Hi, after installing nt, I get: NOTE1: Code tested with python 2.7.3. Your version: 2.7.12 (default, Nov 19 2016, 06:48:10) [GCC 5.4.0 20160609] NOTE2: Please be sure to use the same version of CGenFF in your simulations that was used during parame

[gmx-users] CHARMM2GMX

Hi, after installing nt, I get: NOTE1: Code tested with python 2.7.3. Your version: 2.7.12 (default, Nov 19 2016, 06:48:10) [GCC 5.4.0 20160609] NOTE2: Please be sure to use the same version of CGenFF in your simulations that was used during parameter generation: --Version of CGenFF detecte

Re: [gmx-users] peptide ligand

Dear Justin Thank you so much for all of your help best Farial From: Justin Lemkul To: gmx-us...@gromacs.org Sent: Wednesday, 4 October 2017, 15:19:38 Subject: Re: [gmx-users] peptide ligand On 10/3/17 1:51 PM, farial tavakoli wrote: >  blockquote, div.yahoo_quoted { margin-left

Re: [gmx-users] ERROR in cgenff_charmm2gmx.py

Cheers Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofact

Re: [gmx-users] CR atom name CHARMM27 ff

On 10/4/17 7:30 AM, Sergio Manzetti wrote: Hi , I have tried to convert the mol2 to ITP by protparam.org, and apparently it works, nevertheless it gives a CR atom for alkane carbons. This CR is not in the charm27 ff atomtypes. What is the correct name for this? If you're getting a force fi

Re: [gmx-users] ERROR in cgenff_charmm2gmx.py

On 10/4/17 7:11 AM, Sergio Manzetti wrote: Hi Justin, can [ http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/cgenff_charmm2gmx.py | cgenff_charmm2gmx.py ] do full charges? I get an error: Traceback (most recent call last): File "./charmm2gmx.py", line 47, in impor

Re: [gmx-users] continue simulation from intermediate frame instead of last frame

On 10/4/17 6:26 AM, tarak karmakar wrote: Hi All, Is there any way to continue a simulation from an intermediate time scale, (say, from a frame at time=180 ns instead of 190.772 ns)? Only if you have the .cpt file that corresponds to that frame. -Justin gmx_mpi_d convert-tpr -s topol.tpr

Re: [gmx-users] checking simulation time

On 10/4/17 3:22 AM, Bukunmi Akinwunmi wrote: thanks Justin and Tasneem. but how do i retrieve the log file from an ongoing simulation. all I have is the job id because I am using a cluster for the calculation. Well, the output is being written somewhere, so that's where you go looking. -J

Re: [gmx-users] peptide ligand

On 10/3/17 1:51 PM, farial tavakoli wrote: blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Because in tuturial , energygroups = protein JZ4So I think ,I have to seperate m

Re: [gmx-users] peptide ligand

On 10/3/17 1:46 PM, farial tavakoli wrote: blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Oh I am sorry. Yes  I am trying to run md on my protein peptide complex. At first

[gmx-users] CR atom name CHARMM27 ff

Hi , I have tried to convert the mol2 to ITP by protparam.org, and apparently it works, nevertheless it gives a CR atom for alkane carbons. This CR is not in the charm27 ff atomtypes. What is the correct name for this? Thanks Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ htt

[gmx-users] ERROR in cgenff_charmm2gmx.py

Hi Justin, can [ http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/cgenff_charmm2gmx.py | cgenff_charmm2gmx.py ] do full charges? I get an error: Traceback (most recent call last): File "./charmm2gmx.py", line 47, in import networkx as nx ImportError: No module nam

Re: [gmx-users] Topolgen and topolbuild

Thanks which of the CHARMM FFs from GMX library is correct for a fluorinated molecule? Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 5769

[gmx-users] Topolgen and topolbuild

Hi Sergio If you have the str file for your molecule, it is straightforward to obtain the itp, since you have all the parameters you need to construct a rtp files. You have to download the charmm ff parameters for gromacs available here http://mackerell.umaryland.edu/~kenno/cgenff/program.php#

Re: [gmx-users] Topolgen and topolbuild

On 10/4/17 6:09 AM, Sergio Manzetti wrote: Hi Stephane. Thanks for that. I have tried it, however it generates a str file, and from there how to generate the GMX ITP is unknown. Is there a tutorial that shows how to generate ITP from STR? Use our conversion script: http://mackerell.umaryla

[gmx-users] continue simulation from intermediate frame instead of last frame

Hi All, Is there any way to continue a simulation from an intermediate time scale, (say, from a frame at time=180 ns instead of 190.772 ns)? gmx_mpi_d convert-tpr -s topol.tpr -f state_prev.cpt -e ener.edr -time 18 -o topol.tpr gmx_mpi_d mdrun -s topol.tpr -noappend This does not help as it r

[gmx-users] Generate GROMACS topology

PS: For those silent wonderers on this topic, SWISSPARAM can do the trick: https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=24554 Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ]

Re: [gmx-users] Topolgen and topolbuild

PS: generate ITP from STR without CHARMM GUI Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab  ]

Re: [gmx-users] Topolgen and topolbuild

Hi Stephane. Thanks for that. I have tried it, however it generates a str file, and from there how to generate the GMX ITP is unknown. Is there a tutorial that shows how to generate ITP from STR? Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjord

[gmx-users] Topolgen and topolbuild

Hi if your molecule is a ligand, you could use ParamChem (https://cgenff.paramchem.org/) Stéphane -- Message: 1 Date: Wed, 4 Oct 2017 10:10:24 +0200 (CEST) From: Sergio Manzetti To: gmx-users Subject: [gmx-users] Topolgen a

[gmx-users] force field for acetylated protein pdb file

Hi! I acetylated K40 my heterodimer's PDB file using PyTMs in PyMOL. Now I need to simulate it using GROMACS. Which force field would be the best for this purpose? Thank you in advance! Regards, Raag -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/M

[gmx-users] Topolgen and topolbuild

Hi, I found these tow programs on GMX site, however they don't work. How can I generate a CHARMM topology to be used in GMX for a charged molecule? Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtu

Re: [gmx-users] checking simulation time

thanks Justin and Tasneem. but how do i retrieve the log file from an ongoing simulation. all I have is the job id because I am using a cluster for the calculation. Best Regards, Bukunmi -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-

Re: [gmx-users] C++ xtc interface

On 02/10/17 23:16, Adriaan Riet wrote: Hello, I would like to do some work with xtc output files, but I'm having trouble. The documentation has the following functions: /* All functions return 1 if successful, 0 otherwise */ extern int open_xtc(XDR *