[gmx-users] on g_covar to produce average structure

Dear All, The on-line tutorial says, Warning – Average structures (by g_covar) tend to be crude. Minimization is recommended. Here the minmization should be the energy minization step before the NVT and NPT equilibration steps, for our preparation of the files for the production md, right?

[gmx-users] RE：Re: Tabulated potentials

Dear Mark， I used mdrun -rerun. My table reproduced the potential and force. Best, Zhengcai Date: Sat, 23 May 2015 11:55:22 + From: Mark Abraham mark.j.abra...@gmail.com To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users]

[gmx-users] Different Cv and Cp

Hi, I do not know why I obtain two difference cp and cv from NVT and NPT simulations. What I do is, I take 1000 lutidne molecules, and I do firstly an energy minimization with steep integrator, then NPT simulation at T=300 and P=1 atm for 10ns, (I obtain Cp= 230), then I run NVT for 10 ns with

[gmx-users] different Cv and Cp in liquid phase

Hi, I do not know why I obtain two difference cp and cv from NVT and NPT simulations. What I do is, I take 1000 lutidne molecules, and I do firstly an energy minimization with steep integrator, then NPT simulation at T=300 and P=1 atm for 10ns, (I obtain Cp= 230), then I run NVT for 10 ns with

Re: [gmx-users] tpr file portability

Hi! Mark Abraham писал 21-05-2015 12:44: Hi, There are no known issues with .tpr file portability. By design there should be none. Except running file generated with newer version in older version of GROMACS. Mark On Thu, May 21, 2015 at 11:41 AM Satyabrata Das satyabrata...@gmail.com

Re: [gmx-users] tpr file portability

That is not portability but forward compatibility. Not easy to do. Victor 2015-05-25 7:25 GMT-05:00 Alexey Shvetsov ale...@omrb.pnpi.spb.ru: Hi! Mark Abraham писал 21-05-2015 12:44: Hi, There are no known issues with .tpr file portability. By design there should be none. Except

Re: [gmx-users] tpr file portability

Hi, Indeed, by portability I was referring to cross-platform behaviour. Version compatibility is indeed a tricky business - old code cannot in general implement new functionality, and so for many years mdrun has refused to run a .tpr more recent than itself. We do try to keep backward

[gmx-users] Fwd: Different Cv and Cp

Dear Andre, The heat capacity of liquids at constant pressure is approximately the same as heat capacity at constant volume. From my simulations they are different around 50 j/mol.K, that is too much. Best regards On Mon, May 25, 2015 at 2:44 PM, André Farias de Moura mo...@ufscar.br wrote:

[gmx-users] detailed force output from gromacs

Dear gromacs community, Is there a way to get the detailed force components from a simple Ewald analysis? I am interested in the individual contribution by real space, fourier and the intra-correction terms. g_traj -f traj.trr -of merely gives me total force which is not useful for me. If

Re: [gmx-users] g_clustsize

Hi, If the cluster size is constant, what is there to analyze? Mark On Mon, May 25, 2015 at 4:13 PM pratibha kapoor kapoorpratib...@gmail.com wrote: Thanks Mark for your reply. I would like to extract chain ids of all the members of the maximum populated cluster at each point of time. Thus,

Re: [gmx-users] Can we convert one job into many serial jobs?

Hi, On Mon, May 25, 2015 at 4:08 PM Zhang, Cheng c.zhang...@ucl.ac.uk wrote: Dear GROMACS, I am now using openmpi nodes to run GROMACS (e.g. mdrun_mpi) on our cluster. When the nodes required are too many (e.g. more than 8), jobs always take a long time to wait in the queue. So I wonder if

Re: [gmx-users] Doubt about correct system preparation sequence when protonation state calculation and ligand presence are involved

On 5/24/15 1:21 PM, Gustavo Avelar Molina wrote: Hi everyone, I'm a little confused about the most correct sequence of the minimization, equilibration, solvatation and neutralization steps when I need to simulate a protein in a specific pH (through the protonation state calculation in this pH

[gmx-users] Renaming of the chains in time of simulation (like ABC...to X)

Dear GROMACS users and experts, My protein is a trimer (ABC) and I am running md : on binding of a small peptide (chain-D) to a trimer (chain ABC). The peptide binds with both A and B (that means near interface region) I am following the lysozyme tutorial to build the run. I completed the run,

Re: [gmx-users] Tabulated potentials

Hi, OK that's a good start. Check also at long range, and consider using the dispersion correction (iirc maybe it does some numerical integration of the table?), or maybe really long cutoffs. Assuming your wrong-pressure result is reproducible from different starting velocities, then it could

Re: [gmx-users] g_clustsize

I would like to enlist the chain ids (A,B,C...) , of all those which are in cluster at each time frame. Thanks in advance On Mon, May 25, 2015 at 7:43 PM, pratibha kapoor kapoorpratib...@gmail.com wrote: Thanks Mark for your reply. I would like to extract chain ids of all the members of the

Re: [gmx-users] Different Cv and Cp

Are you running with the Berendsen thermostat or barostat? The gromacs g_energy functions for heat capacity use the fluctuation formula, and the fluctuations with both of these algorithms are wrong (as should be printed in the log file warning message). Make sure you use ensemble-preserving

Re: [gmx-users] g_clustsize

Thanks Mark for your reply. I would like to extract chain ids of all the members of the maximum populated cluster at each point of time. Thus, I have created a script that would run g_clustsize at each time frame which is giving me error: Fatal error: Lo: 0.00, Mid: 16.00, Hi: 16.00

Re: [gmx-users] Editconf error

Finally i' ve make it work. As Justin said, there was a problem with 2 atoms of my pdb file and when de .gro file was created show the legend nan in the bad atoms positions. That create the further problem with the editconf command. I would like to thank Justin for their time and effort to solve

Re: [gmx-users] on g_covar to produce average structure

On 5/25/15 1:44 AM, Brett wrote: Dear All, The on-line tutorial says, Warning – Average structures (by g_covar) tend to be crude. Minimization is recommended. Here the minmization should be the energy minization step before the NVT and NPT equilibration steps, for our preparation of the

[gmx-users] Error using grompp - atomtype not found

Hi, I have made a molecule.itp, which is what I want to run MD calculations on. Meaning I couldn't produce it with pdb2gmx but I rather made a .top with vi editor. When I try to use grompp it says atomtype opls_ not found. I have added all the needed atoms in atomtypes.atp of the ff I

[gmx-users] Can we convert one job into many serial jobs?

Dear GROMACS, I am now using openmpi nodes to run GROMACS (e.g. mdrun_mpi) on our cluster. When the nodes required are too many (e.g. more than 8), jobs always take a long time to wait in the queue. So I wonder if there is a possibility that we can 1) convert the job into many serial jobs?

Re: [gmx-users] Different Cv and Cp

Dear Andre, thank you for the link, you are probably right, It seems that my molecule has the difference Cp-Cv in the same range as benzene (since it has also ring structure). Best regards On Mon, May 25, 2015 at 4:44 PM, Faezeh Pousaneh fpoosa...@gmail.com wrote: Dear Michael, I use

Re: [gmx-users] Different Cv and Cp

Dear Michael, I use Parrinello-Rahman for barostat and v-rescale for thermostat. Sorry, could you explain more the second paragraph please? I did not get the method. What I checked so far is checking if gromacs correctly gives Cv,Cp= Var(Energy or Enthalpy)/kBT^2 , and I find that it gives.

Re: [gmx-users] detailed force output from gromacs

Hi, On Mon, May 25, 2015 at 4:00 PM Isabel Constantine isabel.constantine@gmail.com wrote: Dear gromacs community, Is there a way to get the detailed force components from a simple Ewald analysis? Not directly. Writing each force component to its own memory and then adding each

Re: [gmx-users] Error using grompp - atomtype not found

On 5/25/15 11:08 AM, Sotirios Dionysios I. Papadatos wrote: Hi, I have made a molecule.itp, which is what I want to run MD calculations on. Meaning I couldn't produce it with pdb2gmx but I rather made a .top with vi editor. When I try to use grompp it says atomtype opls_ not found. I

Re: [gmx-users] on the command gmx distance

On 5/25/15 3:48 AM, Brett wrote: Dear All, Suppose I have completed a production MD, and I want to get the distance of OD1 of ASP204 in chain G and NH1 of ARG42 in chain A for the last 5 ns in the MD, will you please tell me the detailed command of gmx distance (how to write the input file

[gmx-users] short-range eletrostatic energy of every aminoacid

Hello guys, I'd like to do make an energy matrix of every aminoacid of a simulation of two interacting proteins. I know enemat can assess the matrix, but for this I have to define energygroups in .mdp files. What would be the easiest way to achieve this? Thanks in advance. Regards, Diogo --

Re: [gmx-users] short-range eletrostatic energy of every aminoacid

Hi Diogo, create an index file, either with gmx select or gmx make_ndx, and feed it to grompp. Happy computing, Thomas. -- R. Thomas Ullmann, PhD Theoretical Computational

Re: [gmx-users] g_clustsize

Hi, I don't understand how you can have a problem with one cluster, when the size of that cluster is constant, but the identities of the members of the cluster is not constant. There may be a bug in gmx clustsize, which you might fix or hack around. If not, I guess you have to find a way to have

Re: [gmx-users] Renaming of the chains in time of simulation (like ABC...to X)

Hi, Does the file you're opening in VMD have any information about the chain? You'll need to look at it, e.g. with less. Mark On Mon, May 25, 2015 at 6:44 PM Ambarnil Ghosh ambargrom...@gmail.com wrote: Dear GROMACS users and experts, My protein is a trimer (ABC) and I am running md : on

[gmx-users] Trojan version of putty software

Not gromacs specific, but I thought it was worth posting here. Basically, if you use putty, check the about button and make sure that you don't see the text unidentified build. http://blogs.cisco.com/security/trojanized-putty-software -- Gromacs Users mailing list * Please search the archive

[gmx-users] short-range eletrostatic energy of every aminoacid

Hello guys, I'd like to do make an energy matrix of every aminoacid of a simulation of two interacting proteins. I know enemat can assess the matrix, but for this I have to define energygroups in .mdp files. What would be the easiest way to achieve this? I guess if I am going to find an easier

Re: [gmx-users] CH3CN solvents breaking the periodic box

Dear Cara, Thank you for your answer. I have observed that when I have performed a NVT simulation for this mix solvent box (water 345 and acetonitrile 48), the solvent cavities are generated but in the NPT simulation interestingly there is no void cavity of solvent in solvent box.

Re: [gmx-users] CH3CN solvents breaking the periodic box

On 5/25/15 2:07 PM, Debashis Sahu wrote: Dear Cara, Thank you for your answer. I have observed that when I have performed a NVT simulation for this mix solvent box (water 345 and acetonitrile 48), the solvent cavities are generated but in the NPT simulation interestingly there

Re: [gmx-users] Problem with xpm2ps

On 5/25/15 5:45 PM, Agnivo Gosai wrote: Dear Users I generated the eps file from the do_dssp analysis in GROMACS 4.6.7 using DSSP 2.2.1. The plot area of my post script file is all black and even if I transform it to png using an image converter , the issue is not resolved. My image is given

[gmx-users] Problem with xpm2ps

Dear Users I generated the eps file from the do_dssp analysis in GROMACS 4.6.7 using DSSP 2.2.1. The plot area of my post script file is all black and even if I transform it to png using an image converter , the issue is not resolved. My image is given below :- ​ output.eps

Re: [gmx-users] Renaming of the chains in time of simulation (like ABC...to X)

Hi Mark and GROMACS users, Thanks for your reply. I checked with less but there is no chain information. The file I am loading in VMD: is first *.gro and then loading *.xtc or *.trr files on it. But after loading .gro or .xtc or .trr file ; when I go to the ExtensionsAnalysisSequence

Re: [gmx-users] on the command gmx distance

Hi, On Mon, May 25, 2015 at 7:33 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/25/15 3:48 AM, Brett wrote: Suppose I have completed a production MD, and I want to get the distance of OD1 of ASP204 in chain G and NH1 of ARG42 in chain A for the last 5 ns in the MD, will you please tell me