Re:Re: [gmx-users] MDRun -append error

Hi Roland, Thanks for your reply. My log files are located in the same directory with ''traj.xtc', and the log files are readable by gromacs. I have just find out the solution for my problem. That is because there were also two backup log files named '#md_0_1.log#' and '#md_0_1.edr#' correspond

[gmx-users] Strange problem.complex out of Box after EM

Dear Gromacs users I am trying to simulate a protein complex. That complex has been obtained after protein-protein docking. I have geneated topology, defined box and solvate, added ions successfully. My complex is centered in box. but when I performed Energy minimization then my protein complex

Re: [gmx-users] gromacs/mopac compilation: linking libmopac

Hi all I post here the present status of my query in case my findings may be helpful for someone else. In the case B (using gfortran to compile libmopac) I have some success building g the gromacs binary for mdrun in my x86_64 system. **A Regarding the compilation with ifort, making test wit

[gmx-users] Regarding TIP4P structure

Dear all, Could anybody send me the link for getting the tip4p tip3p and tip5p single water structure in gro/pdb or in anyother format. Thank you. *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- gmx-users mailing listgmx-users@groma

[gmx-users] gromacs/mopac compilation: linking libmopac (Javier Cerezo)

;> >> This time I also get "undefined reference errors", but related to f2c >> funtions: >> +timout.c0x105:)(:. textundefined+ 0x3c8reference) :to undefined` >> do_fioreference' >> totimer.c :`(do_fio.'text >> >> In this case, do

Re: [gmx-users] gromacs/mopac compilation: linking libmopac (Javier Cerezo)

ting the tip4p tip3p and tip5p single water structure in gro/pdb or in anyother format. Thank you. *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/

[gmx-users] Regarding cosine content

Hello all, I have done PCA from 50ns long trajectory for two similar proteins (length 180 aa and RMSD 0.2 A). The equilibration time and final simulation condition were identical for both the protein. But when I checked the cosine content for PC1 for both proteins they were 0.9 and 0.5 respectivel

Re: [gmx-users] Strange problem.complex out of Box after EM

Saba Ferdous wrote: Dear Gromacs users I am trying to simulate a protein complex. That complex has been obtained after protein-protein docking. I have geneated topology, defined box and solvate, added ions successfully. My complex is centered in box. but when I performed Energy minimizat

[gmx-users] Re: Umbrella Sampling - Justin tutorial

Hi Justin, I am sorry for so many questions but I do not understand something. First we run the simulation of pulling Chain A from ChainB with constant force (pull_k1=1000) and constant velocity of pulling (pull_rate1=0.01) We extract windows as we discussed and then run simulations with those con

Re: [gmx-users] Regarding cosine content

Hi Bipin, It seems one of the proteins is taking longer to reach an equilibrium. Maybe it is undergoing a conformational change? Did you calculate the principal components per protein, or for the joint trajectories? It would have been better to echo the commands you used on the list, because it mi

Re: [gmx-users] Regarding cosine content

Thanks for the reply... I calculated principal components per protein using the command g_anaeig -f md.xtc -s md.tpr -v eigenvec.trr -eig eigenval.xvg -comp eigcomp.xvg -rmsf eigrmsf.xvg -2d 2dproj.xvg -proj proj.xvg -tu ns -extr extr.pdb -filt filt.xtc -first 1 -last 2 Also please suggest how one

[gmx-users] Cuda not detected

Hey, I am playing with the gpu version of mdrun and could make it run with: ~/gromacs/gpu/bin/mdrun-gpu -s topol.tpr -device "OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes" However after reboot of the machine ( which is a testing machine) I get the following error: -

Re: [gmx-users] Regarding TIP4P structure

Ravi Kumar Venkatraman wrote: Dear all, Could anybody send me the link for getting the tip4p tip3p and tip5p single water structure in gro/pdb or in anyother format. A single water molecule? Copy and paste the coordinates from the existing .gro files in $GMXLIB. -Justin -

[gmx-users] Re: Umbrella Sampling - Justin tutorial

Steven Neumann wrote: Hi Justin, I am sorry for so many questions but I do not understand something. First we run the simulation of pulling Chain A from ChainB with constant force (pull_k1=1000) and constant velocity of pulling (pull_rate1=0.01) We extract windows as we discussed and then r

Re: [gmx-users] Cuda not detected

try nvidia-smi -a to see whether the GPU card has been correctly configured. This happens on my GPU node. Every time I reboot the computer, I must reconfigure the GPU cards with "nvidia-smi -a" using root account. Ye 2011-11-17 From： Andrzej Rzepiela Date： 2011-11-17 21:01:07 To： gmx-use

[gmx-users] Gromacs 3D maps

Dear all, I'd like to transform an md gromacs trajectory in a 3d maps set. I mean that every 100ps, I need to export frame coordinates to a 3d map. Than I need to compare a map with the following. Could give me any advice about tools/software to use? Additionally I need to export the coordinate (

Re: [gmx-users] Re: Umbrella Sampling - Justin tutorial

Thank you Justin, I will read it for sure and come back to my simulations! Steven On Thu, Nov 17, 2011 at 1:25 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> Hi Justin, >> I am sorry for so many questions but I do not understand something. >> First we run the simulation of pullin

Re: [gmx-users] Cuda not detected

Hey, thank you for the hint. I just finished the tests. The machine is Intel xeon R, 12 cores , 4 Teslas M2090 and 96 gb of memory. I used the most demanding PME dhfr benchmark system ( 7000w + protein) and obtained the following results: 1 cpu core run: 2.135 ns a day 12 cpu cores run: 2

[gmx-users] user contribution

Hallo all, how can I upload a molecule topology? I registered as a user but when I click at the attache file link "this page cannot be changed" appears. Thanks in advance for your help. Thorsten -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-u

[gmx-users] calculate potential with tabulated non-bonded interactions

Dear all, I am trying to calculate potentials for RNA structures with a serial of tabulated potentials (non-bonded). And the only potential I am going to use is the tabulated potentials, and the effect from force field should be removed. However, when I use pdb2gmx to build the topology file, I ha

Re: [gmx-users] Cuda not detected

On 11/17/11 10:10 PM, Andrzej Rzepiela wrote: Hey, thank you for the hint. I just finished the tests. The machine is Intel xeon R, 12 cores , 4 Teslas M2090 and 96 gb of memory. I used the most demanding PME dhfr benchmark system ( 7000w + protein) and obtained the following results: 1 cpu

Re: [gmx-users] calculate potential with tabulated non-bonded interactions

Liu, Liang wrote: Dear all, I am trying to calculate potentials for RNA structures with a serial of tabulated potentials (non-bonded). And the only potential I am going to use is the tabulated potentials, and the effect from force field should be removed. However, when I use pdb2gmx to build

Re: [gmx-users] calculate potential with tabulated non-bonded interactions

Well, I already have the xvg files from others. However I don't know how to use it. On Thu, Nov 17, 2011 at 10:00 AM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> Dear all, >> >> I am trying to calculate potentials for RNA structures with a serial of >> tabulated potentials (non-bonded).

Re: [gmx-users] calculate potential with tabulated non-bonded interactions

Liu, Liang wrote: Well, I already have the xvg files from others. However I don't know how to use it. Start with the manual, where modifications to the topology and relevant commands and files are described. Then refer to the how-to online, which has specific instructions. Then, ask spe

Re: [gmx-users] user contribution

Thorsten Koeddermann wrote: Hallo all, how can I upload a molecule topology? I registered as a user but when I click at the attache file link "this page cannot be changed" appears. Thanks in advance for your help. You have to email Rossen before you can modify anything. His email is link

[gmx-users] Hydrogen database

Hi, I have recently studied the hydrogen database format of .hdb files (page 118, section 5.6.4 in the manual version 4.5.4). I would like to make a few remarks that, if correct, may need addressing. 1) Method 3 of adding the hydrogens, that of two planar hydrogens, gives -NH2 as the example

[gmx-users] Thanks Justin Lemkul

*With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- 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! Pleas

[gmx-users] PMF with nanotube

Hello, I am trying to find the PMF for the diffusion of small molecule through a nanotube. I have generated the umbrella sampling windows from pull_geometry=direction simulation and umbrella sampling with pull_geometry=position. I guess the PMF for this system can be obtained by combining the g_wh

[gmx-users] Re: gmx-users Digest, Vol 91, Issue 119

iddle one or any other? > > > > The second thing I would like to extract starting configurations from > from > > my pulling. Till frame 189 the COM varies from 0.49 to 0.56 - makes sense > > as the ChainA is still within ChainB. I would like to use configurations: > > > > 0

Re: [gmx-users] calculate potential with tabulated non-bonded interactions

Well my first question is: if the pdb2gmx command must take a force file? I guess it should be necessary. Then the available list contains amber and others, but not user-specified potential. This will affect the future simulation or calculation? On Thu, Nov 17, 2011 at 10:06 AM, Justin A. Lemkul

Re: [gmx-users] GROMACS/ORCA QMMM

Hi Cristoph, Thanks for the reply. I found that my problem was not gromacs. The input that ORCA was receiving from GROMACS did not have the correct number of hydrogens. I've solved this problem now and ORCA is running fine. I however ran into another problem with my energy minimization. The o

Re: [gmx-users] Strange problem.complex out of Box after EM

Please change the subject line to the relevant topic and do not paste the entire digest. I guess the archive is already somewhat hopeless, but let's not make it worse :) Saba Ferdous wrote: Dear Justin, I have set 1.5 dodecahedron. i centered the complex in box. complex.gro, complexsol.gro

Re: [gmx-users] calculate potential with tabulated non-bonded interactions

Liu, Liang wrote: Well my first question is: if the pdb2gmx command must take a force file? I guess it should be necessary. Then the available list contains amber and others, but not user-specified potential. This will affect the future simulation or calculation? Yes. Gromacs allows you

Re: [gmx-users] GROMACS/ORCA QMMM

Jose Tusell wrote: Hi Cristoph, Thanks for the reply. I found that my problem was not gromacs. The input that ORCA was receiving from GROMACS did not have the correct number of hydrogens. I've solved this problem now and ORCA is running fine. I however ran into another problem with my ener

[gmx-users] Regarding Shell Molecular Dynamics

Dear All, Is it not possible to minimize using cg with flexible constraints? Thank you In advance. *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo

Re: [gmx-users] GROMACS/ORCA QMMM

Hi Justin, Thanks for the input on why this is happening. It sounds a little suspicious that the energy doesn't change after a few steps of energy minimization. Do you know of any way that I can find out what is going on? Thanks, Jose Tusell On Thu, Nov 17, 2011 at 10:58 AM, Justin A. Lemkul

Re: [gmx-users] GROMACS/ORCA QMMM

Jose Tusell wrote: Hi Justin, Thanks for the input on why this is happening. It sounds a little suspicious that the energy doesn't change after a few steps of energy minimization. Do you know of any way that I can find out what is going on? The screen output should indicate the atom with

[gmx-users] what's the math algorithm?

Dear all, Assuming I have a some tabulated potentials, table.xvg, tablep.xvg, table_P_P.xvg, table_P_C.xvg and so on. Also there are non-zero values in the first column of both table.xvg and tablep.xvg; while the first column (x), the six column (h(x)) and the last column (h'(x)) have non-zero num

Re: [gmx-users] query for energy minimization in solvent

Yes I m using 4.0.7 version.so for that how could I change the name accordingly. On Sat, Nov 5, 2011 at 1:37 AM, Justin A. Lemkul wrote: > > > Anushree Tripathi wrote: > >> when i run the given command i.e, >> >> grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr >> It is showing f

Re: [gmx-users] GROMACS/ORCA QMMM

I'll try changing the step size first and if that fails I'll try another algorithm. Thanks for the input. Jose Tusell On Thu, Nov 17, 2011 at 11:48 AM, Justin A. Lemkul wrote: > > > Jose Tusell wrote: >> >> Hi Justin, >> >> Thanks for the input on why this is happening.   It sounds a little >>

Re: [gmx-users] GROMACS/ORCA QMMM

hello, I am trying to simulate streptavidin tetramer-biotin complex.I ve calculated Ligand topology from a sofware PRODRG using gromos87 force fields.After solvating it,I am getting an error using grompp command Fatal error: Atomtype HW not found can anyone provide me some help? Thanx with antic

[gmx-users] non-specific protein-protein interactions

Dear gromacs list, Does anyone know how well current force fields capture the energetics of non-specific protein-protein interactions? I'm simulating a protein with an arm that alternates between (apparently) non-specific adsorption to the main-body of the protein and free movement in the solvent

Re: [gmx-users] query for energy minimization in solvent

Anushree Tripathi wrote: Yes I m using 4.0.7 version.so for that how could I change the name accordingly. Check ions.itp and use the names required by your chosen force field. -Justin On Sat, Nov 5, 2011 at 1:37 AM, Justin A. Lemkul > wrote: Anushree Tripat

[gmx-users] Poor exchange probability for REMD

Dear GMX users， Recently i am performing the REMD simulation with Gromacs program and the temperature distribution for each replica was predicted with the server "http://folding.bmc.uu.se/remd/";. However, after a 2-ns short test simulation with 64 replicas , i checked the exchange probabili

Re: [gmx-users] Hydrogen database

Most of the issues should wash out after energy minimization anyway, so I wouldn't care about bond angles too much. Just remember: the topology controls the geometry not the hydrogen database. Yes the hdb file format isn't too intuitive but after awhile I figured it out. Here some examples of hy

[gmx-users] analysing helix dynamics

Hi all, During MD simulations of a protein,I find that there are two helices switch periodically from being parallel and perpendicular to each other. I'd like to plot out the orientation of these two helices with respect to each other, is there a command to extract this information? JJ http://ww

[gmx-users] fatal occur occuring

hello, I am trying to simulate streptavidin tetramer-biotin complex.I ve calculated Ligand topology from a sofware PRODRG using gromos87 force fields.After solvating it,I am getting an error using grompp command Fatal error: Atomtype HW not found can anyone provide me some help? Thanx with antic

Re: [gmx-users] fatal occur occuring

swati patel wrote: hello, I am trying to simulate streptavidin tetramer-biotin complex.I ve calculated Ligand topology from a sofware PRODRG using gromos87 force fields.After solvating it,I am getting an error using grompp command Fatal error: Atomtype HW not found can anyone provide me so

[gmx-users] difference in force fields.

helo justin, yess since i am dealing with a complex,so i generated protein topology using gromos96 43a1 force fields and for ligands,obtained topology using PRODRG which uses gromos 87 force fields. How to obtain similar force fields topologies since PRODRG only works with gromos87 force fields a

Re: [gmx-users] difference in force fields.

swati patel wrote: helo justin, yess since i am dealing with a complex,so i generated protein topology using gromos96 43a1 force fields and for ligands,obtained topology using PRODRG which uses gromos 87 force fields. How to obtain similar force fields topologies since PRODRG only works w

[gmx-users] problem in NVT equilibration

While running the command for NVT equilibration,I am getting one warning for nvt.mdp i.e., The sum of the two largest charge group radii(2.334343) is larger than rlist (1.00).But it is working and generating nvt.tpr when I am using -maxwarn option.should I avoid this warning.Otherwise what to d

Re: [gmx-users] problem in NVT equilibration

Anushree Tripathi wrote: While running the command for NVT equilibration,I am getting one warning for nvt.mdp i.e., The sum of the two largest charge group radii(2.334343) is larger than rlist (1.00).But it is working and generating nvt.tpr when I am using -maxwarn option.should I avoid t

[gmx-users] PRODRG2.5 server not found.

Helo Justin, The link for prodrg 2.5 server is i.e. http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta is 404 not found.How should I proceed further? Thanx. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at htt

[gmx-users] problem obtaining similar force fields for protein and ligand

Hello Users, I am facing a problem in obtaining topologies for my ligand.I tried working on acpype,bt it seems very complex to me.PRODRG is easy but it uses gromos87 force field.PRODRG 2.5 is still not available for download. can anyone suggest me how to obtain topologies for my protein and ligan

[gmx-users] Regarding cosine content

Thanks for the reply... I calculated principal components per protein using the command g_anaeig -f md.xtc -s md.tpr -v eigenvec.trr -eig eigenval.xvg -comp eigcomp.xvg -rmsf eigrmsf.xvg -2d 2dproj.xvg -proj proj.xvg -tu ns -extr extr.pdb -filt filt.xtc -first 1 -last 2 Also please suggest how one