[gmx-users] Distance of pull group 1 (2.142226 nm) is larger than 0.49 times the box size (2.184750)

Sir I am studying protein-ligand interaction through umbrella sampling. I used the following value foe md_pull.mdp file pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= Y Y Y pull_start = yes ; define initial COM distance > 0 pull_ngrou

Re: [gmx-users] constant protonation state MD

Thanks a lot Erik and Baptista I am interested in simulating the change in secondary structure which is supposed to be influenced by the change in the pH environment of the cell. Experimentally it is not known but it has been proposed by many that the change in pH leads to change in conformation. I

[gmx-users] keeping water (entirely) out of the bilayer core

Dear users: I am interested in running simulations of lipid bilayers in which I keep all water molecules out of the bilayer core (not just statistically, but absolutely). However, I have been unable to figure out how to do it. I'll list what I have tried in the hope that others have some ideas

Re: [gmx-users] constant protonation state MD

Hi Shahid, As Erik said, it depends... on your system, on the process you are studying in that system, on the property you think it's relevant to study that process, etc. If your question refers to the (de)protonation of acidic and basic groups usually occuring in aqueous solution, there are

[gmx-users] configuration/installation of gromacs-4.6.1 on heterogeneous cluster

Hi, I am struggling with the configuration and compilation/installation of gromacs-4.6.1. Our cluster has 2 different processors: the older generation supports sse4.1, the newer sse4.2. Configuration and compilation must be done on the headnode of the cluster, which supports sse4.2. I am using the

Re: [gmx-users] constant protonation state MD

Yes that's what lambda dynamics does. I mentioned it since it addresses the interplay between protonation and structure. So to answer your original question: it depends. Erik On 3 May 2013, at 15:27, shahid nayeem wrote: > If I know correctly in lambda dynamics the dynamics of > protonation/d

Re: [gmx-users] where can be obtain circled lipids bilayer?

Is it really fair to call this a circle? A circle is a 2D object. What you are describing here is a disc. Jesper On May 2, 2013, at 1:13 PM, Mirco Wahab wrote: > There are indeed "circular lipid bilayer structures" possible, but they are > not found very frequently. See here for example: >

Re: [gmx-users] Umbrella sampling's equilibration runs

On 5/3/13 2:21 PM, James Starlight wrote: Couple extra question about umbrella Does it possible to use Collective variable (eigenvector from EDA or NMA) as the pulling coordinate? Does it possible to use output from essential dynamics sampling (here I can use EDS in targeted mode to pull my st

[gmx-users] Potential energy for partial system

Hi all, I been working on a thin film system. To avoid the surface effect, I would like to collect potential energy data for the central region of the thin film by excluding near-surface & near-substrate molecules. However, I cannot find any straight forward way to achieve that purpose by us

Re: [gmx-users] Error after trjconf processing

The problem was solved by adding -pbc mol -ur compact flags to the trjconv. So the problems were indeed in pbc conditions James 2013/5/3 Mark Abraham > On Fri, May 3, 2013 at 3:17 PM, James Starlight >wrote: > > > Mark, > > > > > > but if I run npt equilibration onto minimized structure (with

Re: [gmx-users] regression tests 4.6.1 with intel 13.0.1

Thank you for pointing out that. I was using regression test 4.6 Now, I tested 4.6.1 regression tests. single precision is fine. Double precision produced two failed tests: vdwalone: ??--[ 13:21:13 ]--\> $ more checkpot.out comparing energy file reference_d.edr and ener.edr There are 40

Re: [gmx-users] Umbrella sampling's equilibration runs

Couple extra question about umbrella Does it possible to use Collective variable (eigenvector from EDA or NMA) as the pulling coordinate? Does it possible to use output from essential dynamics sampling (here I can use EDS in targeted mode to pull my structure to the target conformation) for the um

Re: [gmx-users] regression tests 4.6.1 with intel 13.0.1

Were you using the 4.6.1 regression test package? Mark On May 3, 2013 7:53 PM, "José Luis Gordillo Ruiz" wrote: > Hi, > > I just built gromacs 4.6.1 with intel compilers 13.0.1 on a machine with > Intel E5 2600 CPUs > > After run the regression tests in single precision, I had two failed tests >

[gmx-users] regression tests 4.6.1 with intel 13.0.1

Hi, I just built gromacs 4.6.1 with intel compilers 13.0.1 on a machine with Intel E5 2600 CPUs After run the regression tests in single precision, I had two failed tests (coulandvdwtogether and vdwalone). Both of them reported this: "Different warnings in reference.warn and grompp.warn" and t

[gmx-users] Re: genion

Hi Justin, Yup, the grompp works fine. :) Gotta figure out on the Blowing Up now. (>.<) Thank you once again! Take care. -- View this message in context: http://gromacs.5086.x6.nabble.com/genion-tp5007916p5007924.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. --

Re: [gmx-users] Re: genion

On 5/3/13 11:52 AM, Ewaru wrote: Hi Justin, Thank you for your prompt reply! My grompp goes like this: "grompp -f minim.mdp -c m4_solv_ions.gro -p topol.top -o em.tpr" Is it in the topol.top file? The reason I'm asking this is because I obtained this error while running MD: Yes, you should

Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

Actually pdb which is similarly doesn't have velocity information. In this case however I'm mainly interested to see how the potential terms compare between the two packages with Charmm27 ff. Reza > > > On 5/3/13 11:33 AM, Reza wrote: >> Thanks Mark! >> >>> No, they weren't. See >>> http:

[gmx-users] Re: genion

Hi Justin, Thank you for your prompt reply! My grompp goes like this: "grompp -f minim.mdp -c m4_solv_ions.gro -p topol.top -o em.tpr" Is it in the topol.top file? The reason I'm asking this is because I obtained this error while running MD: "Fatal error: 2 particles communicated to PME node 2

Re: [gmx-users] Re: rotation of a ligand

On 5/3/13 7:56 AM, Ahmet yıldırım wrote: Dear users, I tried to calculate the order parameter of benzene ring of the ligand using g_order but I have a error as the following : make_ndx -f topol.tpr -o order.xvg a C1 C2 C3 C4 C5 C6 Found 6 atoms with names C1 C2 C3 C4 C5 C6 26 C1_C2_C3_C4_C5_

Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

On 5/3/13 11:33 AM, Reza wrote: Thanks Mark! No, they weren't. See http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy You cannot hope to reproduce accurately the energy of a configuration if you let the coordinates be manipulated. The "rerun" option is interesting - in my ca

Re: [gmx-users] genion

On 5/3/13 11:27 AM, Ewaru wrote: Hi, Just wondering. My system shows this: "System has non-zero total charge: 11.98" and thus, I use the command as below to add 12 Cl to the protein: "genion -s ions.tpr -o m4_solv_ions.gro -p topol.top -pname NA -nname CL -nn 12" However, when I checked

Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

Thanks Mark! > No, they weren't. See > http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy > You cannot hope to reproduce accurately the energy of a configuration if > you let the coordinates be manipulated. > The "rerun" option is interesting - in my case however the potential ene

[gmx-users] genion

Hi, Just wondering. My system shows this: "System has non-zero total charge: 11.98" and thus, I use the command as below to add 12 Cl to the protein: "genion -s ions.tpr -o m4_solv_ions.gro -p topol.top -pname NA -nname CL -nn 12" However, when I checked the genion.log file, it shows that th

[gmx-users] Re: where can be obtain circled lipids bilayer? (Björn Sommer)

Hello Albert, our MembraneEditor (Java Webstart) http://cm2.cellmicrocosmos.org has a new plugin available which can be used to build vesicle membranes. http://www.cellmicrocosmos.org/Cmforum/viewtopic.php?f=35&t=676 You have to import it into the MembraneEditor by using "Settings -> Manage

[gmx-users] Re: installation Gromacs-Fedora18

> Date: Fri, 3 May 2013 20:00:57 +0900 > From: Souilem Safa > Subject: Re: [gmx-users] installation Gromacs-Fedora18 > To: Discussion list for GROMACS users > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > many thanks to you all, > I did installation as root it works we

Re: [gmx-users] constant protonation state MD

If I know correctly in lambda dynamics the dynamics of protonation/deprotonation equilibria is accounted for while my question relates to the typical constant protonation MD where each titratable group remains in one protonation state throughout the simulation. Please educate me Shahid On Fri, Ma

Re: [gmx-users] Error after trjconf processing

On Fri, May 3, 2013 at 3:17 PM, James Starlight wrote: > Mark, > > > but if I run npt equilibration onto minimized structure (without > velocities) without definition of the new velocities in the npt.mdp file > > gen_vel = No > > I noticed that in npt.gro file velocities present. Have it been ass

Re: [gmx-users] Error after trjconf processing

Mark, but if I run npt equilibration onto minimized structure (without velocities) without definition of the new velocities in the npt.mdp file gen_vel = No I noticed that in npt.gro file velocities present. Have it been assigned inspite on gen_vel = No in mdp? James 2013/5/3 Mark Abraham

Re: [gmx-users] Error after trjconf processing

EM has no velocities, by definition. Does the EM mdrun write a .gro file with velocities? If so, that's a bug. On Fri, May 3, 2013 at 2:51 PM, James Starlight wrote: > I've noticed that the minimized conformers no longer has the velocities in > gro file (and npt rus without warnings in that case

Re: [gmx-users] constant protonation state MD

I don't have one in mind. It's a delicate question and perhaps I shouldn't have phrased it the way I did. Nevertheless, the pKa of most side chains mean that their protonation will be dominated by one state for most pH values. pKa-shifts and complicated interplay between protonation and structur

Re: [gmx-users] Error after trjconf processing

I've noticed that the minimized conformers no longer has the velocities in gro file (and npt rus without warnings in that case) in comparison to the not-minimized structures ( where velocities were present and gromp sent warnings). All pbc options lare the same for all conformers and box vectors co

Re: [gmx-users] constant protonation state MD

Thanks a lot Erik. Could I get some reference based on which you say that much of the structural biology will be largely unaffected. Shahid On Fri, May 3, 2013 at 1:05 PM, Erik Marklund wrote: > There's no general answer to that. Proton conductivity measurements, for > instance, will be horrib

[gmx-users] Re: rotation of a ligand

Dear users, I tried to calculate the order parameter of benzene ring of the ligand using g_order but I have a error as the following : make_ndx -f topol.tpr -o order.xvg > a C1 C2 C3 C4 C5 C6 Found 6 atoms with names C1 C2 C3 C4 C5 C6 26 C1_C2_C3_C4_C5_C6 : 6 atoms >q g_order -f traj.xtc -s topol.

Re: [gmx-users] Error after trjconf processing

On Fri, May 3, 2013 at 11:15 AM, James Starlight wrote: > Mark, > > thanks for suggestions > > as I've told previously I've removed pbc via trjconv witout -pbc mol and > -pbc > nojump flags I didn't see anything like that in this thread... > (the same way I found in Justin's umbrella tutorial

Re: [gmx-users] installation Gromacs-Fedora18

many thanks to you all, I did installation as root it works well I like gromacs users discussion. It is very useful :) On 3 May 2013 19:10, Francesco wrote: > this is what I do to install gromacs 4.5.5 on fedora 18 > > fftw libraries > > cd fftw-3.3.3_folder > ./configure --enable-threads --ena

Re: [gmx-users] issue in replica exchange

Summarizing! On Fri, May 3, 2013 at 12:31 AM, XAvier Periole wrote: > > Are confirming that you reproduce the problem with gmx-4.6.1 or simply > summarizing in case we lose track :)) > > On May 2, 2013, at 23:31, Michael Shirts wrote: > >> So to summarize -- the problem appears to be with parti

[gmx-users] Proteins with ADP & ATP cofactors

Dear all, Does anybody have the parameters files for ATP and ADP for the AMBER03 ff? Alternatively, I know that I can find the corresponding files on the AMBER package web-site http://www.pharmacy.manchester.ac.uk/bryce/amber#cof but I don't know how convert these files so I can use them with GR

Re: [gmx-users] distance of pull group 1 is larger than the box size

On 5/3/13 12:10 AM, Arunima Shilpi wrote: Hello sir I got the following error while running pulling mdrun -s pull.tpr "distance of pull group 1 is larger than the box size" I request you to kindly guide me in overcoming the error Since we know nothing of what you are doing or how you ar

Re: [gmx-users] installation Gromacs-Fedora18

this is what I do to install gromacs 4.5.5 on fedora 18 fftw libraries cd fftw-3.3.3_folder ./configure --enable-threads --enable-shared --enable-float --prefix=/usr/local/fftw make make install make clean in this way I install single precision (--enable-float) fftw libraries in /usr/local/fftw

Re: [gmx-users] Simulation of Small Water Box

On 5/3/13 5:41 AM, Monoj Mon Kalita wrote: Dear Users Can Anybody help me to simulate a water box with nearly 14.45 A box size and approximately 93 water molecules. I have tried to simulate it using the 'spc' water model. I have done the SD and CG minimization step. Till that step it was fine

Re: [gmx-users] installation Gromacs-Fedora18

On 5/3/13 5:39 AM, Souilem Safa wrote: Dear Gromacs users, I m aiming to install gromacs 4.5.5 package in in linux Fedora 18. I have updated the needed compilers and downloaded the fftw-3.3.2.tar.gz and gromacs4.5.5.tar.gz I have followed these commands to install: $ tar -zxvf fftw-3.3.2/ $ cd

[gmx-users] Simulation of Small Water Box

Dear Users Can Anybody help me to simulate a water box with nearly 14.45 A box size and approximately 93 water molecules. I have tried to simulate it using the 'spc' water model. I have done the SD and CG minimization step. Till that step it was fine, but when I tried to do MD then I got the foll

[gmx-users] installation Gromacs-Fedora18

Dear Gromacs users, I m aiming to install gromacs 4.5.5 package in in linux Fedora 18. I have updated the needed compilers and downloaded the fftw-3.3.2.tar.gz and gromacs4.5.5.tar.gz I have followed these commands to install: $ tar -zxvf fftw-3.3.2/ $ cd fftw-3.3.2/ $ ./configure --prefix /home/s

Re: [gmx-users] Error after trjconf processing

Mark, thanks for suggestions as I've told previously I've removed pbc via trjconv witout -pbc mol and -pbc nojump flags (the same way I found in Justin's umbrella tutorial where conformers were extracted from pulling trajectory). Might it be source of the some artifacts with pbc ? so if I unders

Re: [gmx-users] random seed in molecular dynamics

gen_vel controls the generation of random velocities. grompp follows it (but I'd have to check the code to see what it does if you use grompp -t). tprconv does not follow it. The random seed is in a different variable, but only does anything if gen_vel=yes. I am not sure what the basis of your co

Re: [gmx-users] Error after trjconf processing

Trajectory frames written by mdrun are not post-processed to guess how you would like PBC to be treated for whatever purpose you have next. So if a molecule straddles a periodic boundary given the current center position, that's what it looks like. If there are things you want to do, then there's t

Re: [gmx-users] random seed in molecular dynamics

If I recall correctly it uses the seed provided in the mdp file. If no seed is provided it uses the process id for seeding. The manual explains the details. Erik On 3 May 2013, at 08:00, Preeti Choudhary wrote: > hey this is regarding random seed used in md.this is when it selects the > intia

Re: [gmx-users] constant protonation state MD

There's no general answer to that. Proton conductivity measurements, for instance, will be horribly wrong without dynamic protonation. Much (but not all) structural biology, however, will be largely unaffected. Erik On 3 May 2013, at 04:30, shahid nayeem wrote: > Dear all > > Can someone enl