Re: [gmx-users] concatenating 2 xtc files

Hi Kavya, That shouldn be a problem. Please post your sequence of commands for concatenating and further processing of the trajectory. Cheers, Tsjerk On Thu, Aug 1, 2013 at 8:12 AM, Kavyashree M wrote: > Dear users, > > I ran a simulation for 25ns. First 5ns in 8 core machine > and late part

[gmx-users] concatenating 2 xtc files

Dear users, I ran a simulation for 25ns. First 5ns in 8 core machine and late part in 64 cores. It ran without any problem. The trajectories were concatenated, jumps are removed and rmsd was calculated. But there was sudden jump in the rmsd curve. Is it wrong to run simulations in different cores

[gmx-users] Potential Energy Scan

Dear All, Can anyone guide me how to perform the 'potential energy scan' for a dihedral of a small molecule in gromacs? Regrads, Tarak -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Sup

Re: [gmx-users] Re: inconsistent energy drops

On 7/31/13 4:45 PM, Brad Van Oosten wrote: looking at the first 2 peaks, they are created from single outlying points in the trajectory. Visually, I can see no discernible difference between it and the frame before/after with the higher energy. To find the source, you'll probably have to fur

[gmx-users] fatal error with charmm/amber forcefield

Dear Gromacs users,   I am using gromacs 4.5.4 .  Is there any known issue/problem in running hamiltonian replica exchange calculations or FEP  with charm27.ff or amber forcefield  in gromacs4.5.4 ? I tried running an hamiltonian replica exchange using charmm27.ff by interpolating A state and B

Re: [gmx-users] Expanded ensemble simulation died with fatal error: Something wrong in choosing new lambda state with a Gibbs move

Hi Dejun- The basic problem is that for this particular configuration, the current state is the only state with nonzero weight. Note that the state with the second highest weight has weight 10^-7. When it tries to compare weights in single precision, it has a numerical overflow and fails. A few

[gmx-users] Re: inconsistent energy drops

looking at the first 2 peaks, they are created from single outlying points in the trajectory. Visually, I can see no discernible difference between it and the frame before/after with the higher energy. -- View this message in context: http://gromacs.5086.x6.nabble.com/inconsistent-energy-drops-

Re: [gmx-users] Interaction energy between specific residue in a set of residues

On 7/31/13 4:20 PM, Collins Nganou wrote: Dear all, I am looking how I can extract the interaction energy between specific residue in a set of residues. Nonbonded energy terms are decomposed using energygrps in the .mdp file along with suitable index groups. example: I have DT and D

[gmx-users] Re: Interaction energy between specific residue in a set of residues

Hi Tomas, I am sorry to come with this further problem of gromacs. I would like to plot an interaction energy between DT without include DA. But I do not know how to ask make g_energy read my index file. Furthermore, I was interested of the distance between C5-C6 in adjacent DT. But I do not know

[gmx-users] Interaction energy between specific residue in a set of residues

Dear all, I am looking how I can extract the interaction energy between specific residue in a set of residues. example: I have DT and DA residues, I would like to plot only the energy of the DT. I can extract the DT with the index file, But I am missing information on how to plot the energy b

Re: [gmx-users] inconsistent energy drops

On 7/31/13 3:38 PM, Brad Van Oosten wrote: Hello, I am performing a MD simulation on a small molecule in a bilayer. The simulation seems to run smoothly but when i graph the energy i see large changes in energy randomly throughout the run(see graph).

Re: [gmx-users] Re: topology and coordinate file not matching after grompp

On 7/31/13 3:10 PM, chinnu657 wrote: Right, I've understood that now. I've altered all of that. But somehow, the same error message still appears.. Without the command issued, exact error message (copied and pasted from the terminal), and relevant topology snippet, there's nothing anyone c

[gmx-users] Re: Conserved energy ("Conserved En.") in NVT simulation

Thanks for your comments Mark, If I understood correctly, you are saying, that maybe linear drift in "Conserved En." could indicate conservation of that quantity, which we actually should be interested. However, I made meanwhile some additional calculations and noticed that drift in "Conserved

[gmx-users] inconsistent energy drops

Hello, I am performing a MD simulation on a small molecule in a bilayer. The simulation seems to run smoothly but when i graph the energy i see large changes in energy randomly throughout the run(see graph). I have looked at

[gmx-users] Re: topology and coordinate file not matching after grompp

Right, I've understood that now. I've altered all of that. But somehow, the same error message still appears.. -- View this message in context: http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221p5010259.html Sent from the GROMACS Users Forum ma

Re: [gmx-users] Conserved energy ("Conserved En.") in NVT simulation

On Wed, Jul 31, 2013 at 7:47 PM, Janne Hirvi wrote: > Dear gmx-users, > > I have run some tests (especially) for pure water, being able to achieve > pretty much perfect energy conservation in > NVE ensemble (with PME-switch and shifted VDW potential). Great. > Then, just for the test, I continu

Re: [gmx-users] Membrane Curvature calaculation

On 7/31/13 1:38 PM, Nikhil Agrawal wrote: Dear All, How to calculate membrane curvature with function of time in gromacs? what are the parameters that define curvature? mean angle and distance and all ? can anybody help me to solve this problem , because I am new to gromacs..:) Look int

Re: [gmx-users] Re: topology and coordinate file not matching after grompp

On 7/31/13 2:48 PM, chinnu657 wrote: I actually have another problem. When doing my grompp for nvt equilibration, I egt the error, Topology include file "posre.itp" not found. In my topology file I wrote this: ;Include the force field #include "oplsaa.ff/forcefield.itp" ; Include chain topol

[gmx-users] Re: topology and coordinate file not matching after grompp

I actually have another problem. When doing my grompp for nvt equilibration, I egt the error, Topology include file "posre.itp" not found. In my topology file I wrote this: ;Include the force field #include "oplsaa.ff/forcefield.itp" ; Include chain topologies #include "topol_1AKI.itp" #include

[gmx-users] Re: topology and coordinate file not matching after grompp

Thank you very much Justin. It's working fine now :) Really appreciate it. Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221p5010255.html Sent from the GROMACS Users Forum mailing list archive at Nabble.c

[gmx-users] Expanded ensemble simulation died with fatal error: Something wrong in choosing new lambda state with a Gibbs move

Hi all, I'm running an expanded ensemble simulation using gromacs 4.6.3 and it crashed with the error: Fatal error: Something wrong in choosing new lambda state with a Gibbs move -- probably underflow in weight determination. Denominator is: 0 1.002384e+00 idEnumer

[gmx-users] Conserved energy ("Conserved En.") in NVT simulation

Dear gmx-users, I have run some tests (especially) for pure water, being able to achieve pretty much perfect energy conservation in NVE ensemble (with PME-switch and shifted VDW potential). Then, just for the test, I continued to NVT ensemble by using previous .tpr and .cpt files, but the resul

[gmx-users] Membrane Curvature calaculation

Dear All, How to calculate membrane curvature with function of time in gromacs? what are the parameters that define curvature? mean angle and distance and all ? can anybody help me to solve this problem , because I am new to gromacs..:) Thanks in advance, -- -- gmx-users mailing listgmx

Re: [gmx-users] RDF of water

On 7/31/13 12:18 PM, George Patargias wrote: Hi Justin Yes, it does look like Fig. 8.3 in the manual if I choose the OW atoms as the the two groups! So there must be a problem with the choice water-water or SOL-SOL for RDF groups. Indeed there would, because then (with -rdf atom) you're ca

Re: [gmx-users] RDF of water

Hi Justin Yes, it does look like Fig. 8.3 in the manual if I choose the OW atoms as the the two groups! So there must be a problem with the choice water-water or SOL-SOL for RDF groups. Many thanks! > > > On 7/31/13 10:49 AM, George Patargias wrote: >> Hello >> >> I am trying to calculate the

Re: [gmx-users] Re: topology and coordinate file not matching after grompp

On 7/31/13 11:59 AM, chinnu657 wrote: renumber.gro topol_1AKI.itp topol_2CDS.itp I get the feeling yo

[gmx-users] Re: topology and coordinate file not matching after grompp

renumber.gro topol_1AKI.itp topol_2CDS.itp I get the feeling you're not going to be able to see the

Aw: Re: [gmx-users] Umbrella Sampling

I did this with a small molecule and the ions were in the solvent, but associated with the ligand, and conversly if the site has a Mg or something etc...it wouldn't be restrained in the normal posres.itp unless you made one for them.  It is in the end a matter of view, but I am assuming the change

Re: [gmx-users] Re: topology and coordinate file not matching after grompp

On 7/31/13 11:29 AM, chinnu657 wrote: Hi Justin, Oh, I see. I am going to paste my commands here. pdb2gmx -f 1AKI.pdb -o 1AKI_conf.gro -water spce pdb2gmx -f 2CDS.pdb -o 2CDS_conf.gro -water spce editconf -f 1AKI_conf.gro -o conf1.gro -center 2.5 0 0 editconf -f 2CDS_conf.gro -o conf1.

[gmx-users] Re: topology and coordinate file not matching after grompp

Hi Justin, Oh, I see. I am going to paste my commands here. pdb2gmx -f 1AKI.pdb -o 1AKI_conf.gro -water spce pdb2gmx -f 2CDS.pdb -o 2CDS_conf.gro -water spce editconf -f 1AKI_conf.gro -o conf1.gro -center 2.5 0 0 editconf -f 2CDS_conf.gro -o conf1.gro -center 7.5 0 0 cat conf1.gro conf2.gro

Re: [gmx-users] RDF of water

On 7/31/13 10:49 AM, George Patargias wrote: Hello I am trying to calculate the RDF of water with water for a 10 ns MD of pure SPC water simulation (3x3x3 nm box). I run g_rdf with the default -rdf option (atom). The problem is that the integration of the RDF curve up to the first minimum yie

Re: Fwd: [gmx-users] umbrella Sampling and PMF- Error estimation

On 7/31/13 10:19 AM, Mohsen Ramezanpour wrote: Dear Dr.Justin I read that article, It was very helpful. Thanks a lot. After using g_wham with bootstrapping options. I have got an averaged PMF profile (like Fig.2C in that article) and an standard deviation (like Fig.2D In that article) which ob

Re: [gmx-users] Re: topology and coordinate file not matching after grompp

On 7/31/13 10:07 AM, chinnu657 wrote: Thanks Justin. So, I've understood how to calculate the number of coordinates. That in the topology file matches the amount I calculated (as per how you just taught me). I want to put 2 proteins in the same box. I did this by changing the topology files of

Re: [gmx-users] Problems with REMD in Gromacs 4.6.3

On Fri, Jul 19, 2013 at 6:59 PM, gigo wrote: > Hi! > > > On 2013-07-17 21:08, Mark Abraham wrote: >> >> You tried ppn3 (with and without --loadbalance)? > > > I was testing on 8-replicas simulation. > > 1) Without --loadbalance and -np 8. > Excerpts from the script: > #PBS -l nodes=8:ppn=3 > seten

[gmx-users] RDF of water

Hello I am trying to calculate the RDF of water with water for a 10 ns MD of pure SPC water simulation (3x3x3 nm box). I run g_rdf with the default -rdf option (atom). The problem is that the integration of the RDF curve up to the first minimum yields a zero value which is obviously not right Do

Re: [gmx-users] GROMACS 4.6.3 Static Linking

On Thu, Jul 25, 2013 at 5:55 PM, Mark Abraham wrote: > That combo is supposed to generate a CMake warning. > > I also get a warning during linking that some shared library will have > to provide some function (getpwuid?) at run time, but the binary is > static. That warning has always popped up f

Fwd: [gmx-users] umbrella Sampling and PMF- Error estimation

Dear Dr.Justin I read that article, It was very helpful. Thanks a lot. After using g_wham with bootstrapping options. I have got an averaged PMF profile (like Fig.2C in that article) and an standard deviation (like Fig.2D In that article) which obtained in this way. As you see, the standard deviat

[gmx-users] Re: topology and coordinate file not matching after grompp

Thanks Justin. So, I've understood how to calculate the number of coordinates. That in the topology file matches the amount I calculated (as per how you just taught me). I want to put 2 proteins in the same box. I did this by changing the topology files of the respective proteins to itp. Then a ne

[gmx-users] Re: generating user-defined topologies for surfaces

perfect! -- View this message in context: http://gromacs.5086.x6.nabble.com/generating-user-defined-topologies-for-surfaces-tp5010192p5010235.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/m

Re: [gmx-users] Re: generating user-defined topologies for surfaces

On 7/31/13 8:57 AM, Valentina wrote: Sorry, still confused here: I have a cell, that is same as residue, contains an inorganic crystal. But since I am creating a surface I have bonds going across periodic boundary, like Al and O shown on the pic? Can I still do it? How do I input it into molec

[gmx-users] Re: generating user-defined topologies for surfaces

Sorry, still confused here: I have a cell, that is same as residue, contains an inorganic crystal. But since I am creating a surface I have bonds going across periodic boundary, like Al and O shown on the pic? Can I still do it? How do I input it into molecule.rtp? Thank you, V

Re: [gmx-users] Umbrella Sampling

I am do not want to choose different pulling conditions as I build a model for specific force constant and pulling rate in given force filed. I think restraining would help much more to then exclude the ions impact. Steven On Wed, Jul 31, 2013 at 12:49 PM, Steven Neumann wrote: > Thank you a lo

Re: [gmx-users] Umbrella Sampling

Thank you a lot! On Wed, Jul 31, 2013 at 12:46 PM, Justin Lemkul wrote: > > > On 7/31/13 6:52 AM, Steven Neumann wrote: > >> But even though on the other hand that could be more realistic free energy >> which could be compare to experiment which also involves ions. Would >> Justin >> please com

Re: [gmx-users] Umbrella Sampling

On 7/31/13 6:52 AM, Steven Neumann wrote: But even though on the other hand that could be more realistic free energy which could be compare to experiment which also involves ions. Would Justin please comment on this? I can offer you nothing more than a hand-waving explanation of what I think

Re: [gmx-users] umbrella Sampling and PMF- Error estimation

Thank you for your reply Dr. Justin On 7/31/13, Justin Lemkul wrote: > > > On 7/31/13 7:00 AM, Mohsen Ramezanpour wrote: >> Hi everyone >> >> How can we have an error estimation for Gibbs binding free energy when >> I do umbrella sampling and PMF profile? >> >> Actually I did an umbrella sampling

Re: [gmx-users] umbrella Sampling and PMF- Error estimation

On 7/31/13 7:00 AM, Mohsen Ramezanpour wrote: Hi everyone How can we have an error estimation for Gibbs binding free energy when I do umbrella sampling and PMF profile? Actually I did an umbrella sampling for protein and ligand complex and I have a PMF profile now but I do not know how much i

Re: [gmx-users] topology and coordinate file not matching after grompp

On 7/31/13 6:04 AM, chinnu657 wrote: Hello, I have a problem and although I've read almost everything the internet could offer on how differently people have approached this problem, mine hasn't been solved yet. Basically, I am trying to mix 2 different proteins in one box and after doing my

Re: [gmx-users] vdwtype in mdp file for LIE method

On 7/31/13 3:59 AM, Mark Abraham wrote: What does your background reading suggest is a good choice for VDW type? In addition, what does the chosen force field require? -Justin Mark On Wed, Jul 31, 2013 at 9:18 AM, Mahboobeh Eslami wrote: hi all freind what is vdwtype in mdp file for LI

[gmx-users] umbrella Sampling and PMF- Error estimation

Hi everyone How can we have an error estimation for Gibbs binding free energy when I do umbrella sampling and PMF profile? Actually I did an umbrella sampling for protein and ligand complex and I have a PMF profile now but I do not know how much is my error! Thanks in advance for any suggestion

Re: [gmx-users] Umbrella Sampling

But even though on the other hand that could be more realistic free energy which could be compare to experiment which also involves ions. Would Justin please comment on this? On Wed, Jul 31, 2013 at 11:46 AM, Steven Neumann wrote: > They do not dissociate...Are you sure? My mdp specifies only li

Re: [gmx-users] Umbrella Sampling

They do not dissociate...Are you sure? My mdp specifies only ligand as a pull_group1. I think it would change having ions in this group included. On Wed, Jul 31, 2013 at 11:01 AM, lloyd riggs wrote: > > >will get the PMF profile for my > >ligand binding or ligand and two ions binding? > > It wo

[gmx-users] topology and coordinate file not matching after grompp

Hello, I have a problem and although I've read almost everything the internet could offer on how differently people have approached this problem, mine hasn't been solved yet. Basically, I am trying to mix 2 different proteins in one box and after doing my grompp to neutralise the system, I get th

Aw: [gmx-users] Umbrella Sampling

  >will get the PMF profile for my >ligand binding or ligand and two ions binding?   It would be the ligand and two ions unless the ions also at some point discossiate from the ligand once in solvent. Could add positional restraint for them, but dont know how that effects the calculation? Gese

[gmx-users] probabilty density of C5-C6 bond of all DNA conformer

Dear Users, I am looking the way to extract the probability density of the C5-C6. I will be very grateful to receive an indication on how to monitor it. Best regards Collins -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search th

Re: [gmx-users] Regarding gromos method in g_cluster

Now got the point. Thank you Tsjerk Sir and Prof. David for the help. On Wed, Jul 31, 2013 at 1:42 PM, Tsjerk Wassenaar wrote: > Hi Bipin, > > If A/C have RMSD 0.4 nm, but A/B and B/C both have RMSD < 0.3 nm, they'll > end up in the same cluster. > > Cheers, > > Tsjerk > > > On Wed, Jul 31, 201

Re: [gmx-users] Regarding gromos method in g_cluster

Hi Bipin, If A/C have RMSD 0.4 nm, but A/B and B/C both have RMSD < 0.3 nm, they'll end up in the same cluster. Cheers, Tsjerk On Wed, Jul 31, 2013 at 9:45 AM, bipin singh wrote: > Thanks for the reply Prof. David. But in the output it shows that "The RMSD > ranges from 0.0602553 to 0.411066

Re: [gmx-users] Regarding gromos method in g_cluster

On 2013-07-31 09:45, bipin singh wrote: Thanks for the reply Prof. David. But in the output it shows that "The RMSD ranges from 0.0602553 to 0.411066 nm"; this is the point of confusion to me. So I think it should write the snapshots having RMSD greater than 0.3nm (cutoff) to another cluster. I s

Re: [gmx-users] vdwtype in mdp file for LIE method

What does your background reading suggest is a good choice for VDW type? Mark On Wed, Jul 31, 2013 at 9:18 AM, Mahboobeh Eslami wrote: > hi all freind > what is vdwtype in mdp file for LIE method in free energy calculation? > best regard > -- > gmx-users mailing listgmx-users@gromacs.org > h

Re: [gmx-users] Regarding gromos method in g_cluster

Thanks for the reply Prof. David. But in the output it shows that "The RMSD ranges from 0.0602553 to 0.411066 nm"; this is the point of confusion to me. So I think it should write the snapshots having RMSD greater than 0.3nm (cutoff) to another cluster. On Wed, Jul 31, 2013 at 12:59 PM, David van

[gmx-users] Umbrella Sampling

Dear Gmx Users, I run SMD to extract the windows for US calculations. The system involves negatively charged ligand and protein. I generated the protein-ligand complex within self assembly MD simulations. I pulled my molecule away and two ions were also detached from the protein surface being att

Re: [gmx-users] Regarding gromos method in g_cluster

On 2013-07-31 07:20, bipin singh wrote: Hello All, I was trying to do clustering on my MD trajectory using gromos method under g_cluster module. I got one doubt regarding the output, as I used the cutoff of 0.3nm for RMSD calculation, I was expecting that all the snapshots which have RMSD less t

[gmx-users] vdwtype in mdp file for LIE method

hi all freind what is vdwtype in mdp file for LIE method in free energy calculation? best regard -- 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