[gmx-users] Output of g_hbond

Hi all, I am trying to caluculate number of hydrogen bond in my system using the following command: g_hbond -f model_frame2000.pdb -s md.tpr -n index_water.ndx -num hbnum.xvg Where the file model_frame2000.pdb is the coordinate from a frame during my MD simulation, and the index file

Re: [gmx-users] Output of g_hbond

On 11/23/11 4:12 PM, Hu Qiu wrote: Hi all, I am trying to caluculate number of hydrogen bond in my system using the following command: g_hbond -f model_frame2000.pdb -s md.tpr -n index_water.ndx -num hbnum.xvg Where the file model_frame2000.pdb is the coordinate from a frame during my M

[gmx-users] Regarding Simulation of KALP-15 in DPPC

*Dear All, I was following the tutorial for simulating KALP-15 in DPPC. I got stuck in step three. Following the instruction, I created the dppc128.gro file using editconf. To remove the initial periodcity I was trying to use trjconv but I could not do it. Please help me in this regard

Re: [gmx-users] do_dssp segmentation fault

Hi, On Nov 23, 2011, at 8:24 AM, Alex Jemulin wrote: > Thanks for your reply > Could you tell me the name of the file to download and how to install it? Please follow the instructions at http://www.gromacs.org/Developer_Zone/Git/Basic_Git_Usage and http://www.gromacs.org/Developer_Zone/Git/Git_T

[gmx-users] T-coupling

Dear Gromacs Users, I need to simulate two protein structures by Gromacs 5.4.0. For protein A, the net charge is zero so I don't add any ions. All the commands work properly unitil mdrun of the A_pr.tpr: mdrun -s A_pr.tpr -o A_pr.trr -c A_b4md.gro -g pr.log -e pr.edr& ==> the error: too many LINC

Re: [gmx-users] T-coupling

On 11/23/11 5:43 PM, sarah k wrote: Dear Gromacs Users, I need to simulate two protein structures by Gromacs 5.4.0. For protein A, the net charge is zero so I don't add any ions. All the commands work properly unitil mdrun of the A_pr.tpr: mdrun -s A_pr.tpr -o A_pr.trr -c A_b4md.gro -g pr.log

[gmx-users] Visualizing g_helixorient output

Dear all, I have a follow up question from this recent post http://www.mail-archive.com/gmx-users@gromacs.org/msg45736.html regarding the visualization of g_helixorient output. According to the post, one needs to use xmgrace with -nxy to view the data properly. I have not got the xmgrace progr

[gmx-users] Generating topology file

Hi GROMACS users, I have used acpype.py to convert parameter and topology file from amber to gromacs but some of the parameters (angle and dihedral)regarding a particular residue having mercury in it was not generating,please help.

Re: [gmx-users] Generating topology file

I am sorry, but because antechamber will only work with these atoms: C, N, O, S, P, H, F, Cl, Br and I, so acype won't work for Hg. A "hack" would be to replace Hg by another allowed element. But this is only to give you a hint of what topology and parameters might look like. Then you have to work

[gmx-users] Re: PDB structure quality

An update: Now for NRG-CING, please see: http://nmr.cmbi.ru.nl/NRG-CING Best, Alan On 3 April 2009 11:31, Alan wrote: > We've recently announced iCing, which includes whatif as well. Please, > take a look at http://nmr.cmbi.ru.nl/cing/Home.html. > > If it happens that your complex is from NM

[gmx-users] gromacs 4.5.3 and GCC 4.1.x

Hi, I want to install standard gromacs 4.5.5 on a new linux machine, prior to installing GPU accelerated gromacs. Looking at the installation instructions I see you recommend not to use GCC 4.1.x series of compilers. A year ago I have installed gromacs 4.5.3 and I don't recall seeing the r

[gmx-users] unity in ffbonded.itp

Dear gromacs developers, I would like to know what is the unity for armonic constraint in ffbonded.itp. In the user manual (Table 5.4) it is written that is kJ mol-1 nm-2 but in the .itp file I read "C C 1 0.1525 259408.0 ; new99" I understand that 0.1525 is the equlibrium distan

[gmx-users] NPT or NVT for calculating averaged experimental parameters

Hi there, Is there any consensus on whether to use NVT or NPT runs for calculating averaged NMR parameters in water at room temperature? I have seen some papers which use NPT, others use NVT. Thanks you, Igor -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/lis

[gmx-users] CHARMMff using GROMACS 4.5.3

Hi all, I am trying to run a simulation of a protein and ligand system using Gromacs 4.5.3 and CHARMMff. prior to running this system I ran the protein as is with out adding the ligand, and the simulation was fine. Ligand parametrization was done using the SwissParam server. when trying to run EM I

[gmx-users] Re: pdb2gmx disulfide bond formation - missing bond, angle, & dihedral types with all GROMOS FFs (Tsjerk Wassenaar)

Hi Tsjerk, Thank you for your advice! grompp does not complain (with all three of the previously mentioned versions of GROMACS), but the processed topology, processed.top, also does not have the terms filled in, as I show below for the bonds section: [ bonds ] ; aiaj functc0

[gmx-users] problem with extr of g_anaeig

Hi!! I am looking my eigenvectors through the extr command of g_anaeig and I found different pdb files for my 1st vector in the following 3 conditions: gromacs-4.5.5/bin/g_anaeig -f file.xtc -s average.pdb -v eigenvec.trr -n index.ndx -extr -nframes 20 -first 1 -last 1 gromacs-4.5.5/bin/g_a

Re: [gmx-users] density

Thanks Prof. Warren From: Dallas Warren To: Discussion list for GROMACS users Sent: Tuesday, November 22, 2011 12:23 AM Subject: RE: [gmx-users] density I don’t do COM calculations, so don’t know directly, but have a read of “g_rdf –h”, method is outlin

[gmx-users] Re: NPT or NVT for calculating averaged experimental parameters

> Hi there, > > Is there any consensus on whether to use NVT or NPT runs for calculating > averaged NMR parameters in water at room temperature? I have seen some > papers which use NPT, others use NVT. > > Thanks you, > Igor There should be no difference as far as the density is reproduced adequat

RE: [gmx-users] Regarding Simulation of KALP-15 in DPPC

What exactly did you try? What was the result? Actually copy and paste the commands and output. Saying it didn't work is insufficient detail for anyone to help you. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 3

[gmx-users] how to edit a .xvg file?

Hi everyone, I wonder if there is any tool similar to trjconv that can be used to edit a .xvg file? I just want to extract selected data points (like taking data every 10 ps when the original .xvg contains data every 1 ps) and to concatenate .xvg files according to the time of data. Thanks, Yun

Re: [gmx-users] gromacs 4.5.3 and GCC 4.1.x

Efrat Exlrod wrote: Hi, I want to install standard gromacs 4.5.5 on a new linux machine, prior to installing GPU accelerated gromacs. Looking at the installation instructions I see you recommend not to use GCC 4.1.x series of compilers. A year ago I have installed gromacs 4.5.3 and I

Re: [gmx-users] unity in ffbonded.itp

francesco oteri wrote: Dear gromacs developers, I would like to know what is the unity for armonic constraint in ffbonded.itp. In the user manual (Table 5.4) it is written that is kJ mol−1 nm−2 but in the .itp file I read "C C 1 0.1525 259408.0 ; new99" The value of 1 in

Re: [gmx-users] CHARMMff using GROMACS 4.5.3

Gideon Lapidoth wrote: Hi all, I am trying to run a simulation of a protein and ligand system using Gromacs 4.5.3 and CHARMMff. prior to running this system I ran the protein as is with out adding the ligand, and the simulation was fine. Ligand parametrization was done using the SwissParam se

Re: [gmx-users] how to edit a .xvg file?

Yun Shi wrote: Hi everyone, I wonder if there is any tool similar to trjconv that can be used to edit a .xvg file? I just want to extract selected data points (like taking data every 10 ps when the original .xvg contains data every 1 ps) and to concatenate .xvg files according to the time

Re: [gmx-users] how to edit a .xvg file?

On 24/11/2011 10:31 AM, Yun Shi wrote: Hi everyone, I wonder if there is any tool similar to trjconv that can be used to edit a .xvg file? I just want to extract selected data points (like taking data every 10 ps when the original .xvg contains data every 1 ps) and to concatenate .xvg files

[gmx-users] Hbond occupancy reference rate

Greeting After doing a gormacs MD simulation and finding Hydrogen bonds,applying Justin script give me the Hbonds occupancy rate,then i have to choose the most representative structure in the simulation and show some of my interesting hydrogen bonds for publication purpose. Should i consider a refe

Re: [gmx-users] Visualizing g_helixorient output

On 23/11/2011 8:59 PM, NG HUI WEN wrote: Dear all, I have a follow up question from this recent post http://www.mail-archive.com/gmx-users@gromacs.org/msg45736.html regarding the visualization of g_helixorient output. According to the post, one needs to use xmgrace with --nxy to view the d

RE: [gmx-users] Visualizing g_helixorient output

Dear Mark, Many thanks for taking the time to answer my question. I've had a look at the link. However, as the g_helixorient output files are a little "unconventional-looking", I am not sure if gnuplot could handle them. This is how my bending.xvg file looks like when I view it on my linux term

Re: [gmx-users] how to edit a .xvg file?

Thanks for the reply. In my case, they are the pullf and pullx files from a COM pulling simulation. So does this mean writing a script would be the best way? Thanks, Yun == == -- Message: 5 Date: Wed, 23 Nov 2011 19:04:33 -0500 F

[gmx-users] Re: how to edit a .xvg file?

Sorry for this question. The bash script turned out to be a one-liner. Yun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (u

Re: [gmx-users] Visualizing g_helixorient output

On 24/11/2011 1:50 PM, NG HUI WEN wrote: Dear Mark, Many thanks for taking the time to answer my question. I've had a look at the link. However, as the g_helixorient output files are a little "unconventional-looking", I am not sure if gnuplot could handle them. This is how my bending.xvg f

Re: [gmx-users] Re: how to edit a .xvg file?

Hi Yun, I would not have expected otherwise :p Would you mind sharing your solution? Cheers, Tsjerk On Nov 24, 2011 4:54 AM, "Yun Shi" wrote: Sorry for this question. The bash script turned out to be a one-liner. Yun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.o

[gmx-users] grompp line too long error

I was trying to setup a simulation for membrane in DPPC lipid bilayer following this tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html I successfully generated the .gro file for the system.But when I tried grompp to generate the .tpr file

Re: [gmx-users] grompp line too long error

On 24/11/2011 3:45 PM, 杨伟 wrote: I was trying to setup a simulation for membrane in DPPC lipid bilayer following this tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html I successfully generated the .gro file for the system.But when I tri

Re: [gmx-users] grompp line too long error

Hi [insert name here], Try putting an empty gurgle.dat in your working directory to see if that is the problem. If it's not, can you provide additional information regarding your system and gromacs installation? Cheers, Tsjerk On Nov 24, 2011 5:50 AM, "杨伟" <20104227...@suda.edu.cn> wrote: I wa

Re: [gmx-users] how to edit a .xvg file?

> > > Dear gmx users, Is centroid to centroid clustering method available in Gromacs? I want to use this method to cluster my molecules? ROB -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.groma

[gmx-users] Re: do remd in npt enmable with warning :pressure scaling more than 1%, mu: 1.01087 1.01087 1.01087

dear teacher, when i do remd in npt enmable , there are mang warning like this “Step 520013 Warning: pressure scaling more than 1%, mu: 1.01311 1.01311 1.01311 Step 520014 Warning: pressure scaling more than 1%, mu: 1.01087 1.01087 1.01087 Step 520014 Warning: pressure scaling more than 1%, mu

[gmx-users] do remd in the npt ensemble:Warning: pressure scaling more than 1%, mu: 333821 333821 333821

dear teacher, when i do remd in the npt ensemble. =md.mdp=== ; Start time and timestep in ps tinit= 0 dt = 0.01 nsteps = 5000 ; For exact run continuation or redoing part of a run ; Temperature coupling

Re: [gmx-users] Rv: g_helixorient question

I only just ask for a brief explanation for each file, thanks anyway, the gmx_helixorient.c could be a good solution. Thanks again for your response. De: Mark Abraham Para: Discussion list for GROMACS users Enviado: martes 22 de noviembre de 2011 13:00 Asunt