[gmx-users] Replica Exchange MD using Gromacs

Dear gmx-users, I am facing some problems while running replica exchange MD using Gromacs. Few seconds after the job submission it ends with the following error message: " Initializing Replica Exchange Repl There are 6 replicas: Multi-checking the number of atoms ... OK Multi-checking the integ

Re: [gmx-users] Replica Exchange MD using Gromacs

On 1/04/2011 6:03 PM, Ruchi Gupta wrote: Dear gmx-users, I am facing some problems while running replica exchange MD using Gromacs. Few seconds after the job submission it ends with the following error message: " Initializing Replica Exchange Repl There are 6 replicas: Multi-checking the num

Re: [gmx-users] dipole moment of a charged peptide

On Thu, 2011-03-31 at 18:03 -0700, Sanku M wrote: > Hi, >I have a long-chain peptide which has a net charge of +5 . I was > wondering whether the g_dipole will give any reasonable dipole moment > for a molecule with a net charge. Is there any suggestion I should > follow regarding calculation

Re: [gmx-users] dipole moment of a charged peptide

Dommert Florian skrev 2011-04-01 09.45: On Thu, 2011-03-31 at 18:03 -0700, Sanku M wrote: Hi, I have a long-chain peptide which has a net charge of +5 . I was wondering whether the g_dipole will give any reasonable dipole moment for a molecule with a net charge. Is there any suggestion I sh

Re: [gmx-users] Replica Exchange MD using Gromacs

On 01/04/2011, at 6:29 PM, Mark Abraham wrote: On 1/04/2011 6:03 PM, Ruchi Gupta wrote: Dear gmx-users, I am facing some problems while running replica exchange MD using Gromacs. Few seconds after the job submission it ends with the following error message: " Initializing Replica Excha

Re: [gmx-users] dipole moment of a charged peptide

On Fri, 2011-04-01 at 09:48 +0200, Erik Marklund wrote: > Dommert Florian skrev 2011-04-01 09.45: > > On Thu, 2011-03-31 at 18:03 -0700, Sanku M wrote: > >> Hi, > >> I have a long-chain peptide which has a net charge of +5 . I was > >> wondering whether the g_dipole will give any reasonable d

[gmx-users] FW: protein split over boundary

From: anahita [mailto:ana_j0...@yahoo.com] Sent: Friday, April 01, 2011 1:13 PM To: 'gmx-users-requ...@gromacs.org' Subject: protein split over boundary Dear user, Hello, I appreciate if somebody help me. During the simulation of my protein I didn't get any error but after 1ns of MD my

[gmx-users] FW: protein split over boundaries

From: anahita [mailto:ana_j0...@yahoo.com] Sent: Friday, April 01, 2011 1:13 PM To: 'gmx-users-requ...@gromacs.org' Subject: protein split over boundary Dear user, Hello, I appreciate if somebody help me. During the simulation of my protein I didn't get any error but after 1ns of MD my

Re: [gmx-users] Umbrella Sampling

Cheers Chris Is the best way to check for convergence; to keep adding in more histograms until the curves converge. Also your comment 'don't remove any data', do you mean to keep histograms that are not so good. Gavin chris.ne...@utoronto.ca wrote: > your comment: > > which should be centred aro

[gmx-users] molecule split over bounderies

Dear user, Hello, I appreciate if somebody help me. During the simulation of my protein I didn’t get any error but after 1ns of MD my molecule was split over boundary in cubic box. it means some part of it enter the other side of the box. At first,For decreasing the cost of simulation, in “editc

Re: [gmx-users] FW: protein split over boundary

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -TAW On Fri, Apr 1, 2011 at 10:53 AM, anahita wrote: > > > > > From: anahita [mailto:ana_j0...@yahoo.com] > Sent: Friday, April 01, 2011 1:13 PM > To: 'gmx-users-requ...@gromacs.org' > Subject: protein split over bound

Re: [gmx-users] Is there still interest in rigid-body simulation?

Welcome :) It is absolutely useful. On Mon, Mar 28, 2011 at 2:32 AM, Adam Herbst wrote: > Hi all, > I have seen a few posts on gmx-users indicating a desire to treat certain > atom groups as rigid bodies in MD simulations. I just started implementing > this, and so far I have it working for tra

Re: [gmx-users] FW: protein split over boundary

Dear user, Tanks for your attention ,I read about trjconv,but I want to know is it necessary  to back to the exact fram befor molecule split happens and then center the molecule by trjconv command? The other point,if you attention to my value”edit conf  d=0.9 and during MD rvdw=1..4” is it broke

Re: [gmx-users] FW: protein split over boundary

ana johari wrote: Dear user, Tanks for your attention ,I read about trjconv,but I want to know is it necessary to back to the exact fram befor molecule split happens and then center the molecule by trjconv command? If the protein starts in the center of the box, just use trjconv in conj

[gmx-users] Setting the C6 LJ term for OPLSA FF

Dear all I need to change sigma and epsilon for non-bonded parameters of the OPLSA FF. In particular I want to set the attractive part of the LJ potential to zero (C6=0). In doing this I have read the manual but unfortunately the reported explanation did not help me. To understand how it work in

Re: [gmx-users] FW: protein split over boundary

dear user, Tanks for your advice, But the mdrun is know on the step of 33562880  but the protein was split at the first 1ns of MD. is it necessary to use “tpbconv” command and extract the *.tpr file just after first 1 ns and  then use trjconv –ur compact as command. Best regards,

[gmx-users] The solvent group Water is not continuous

Dear Justin, I have Fatal Errror:The solvent group Water is not continuous. I look at gmx-users mailing list search. I also have the same problem. You said:( http://lists.gromacs.org/pipermail/gmx-users/2010-January/048344.html) It is exactly what I said; you've proven it. You have solvent, ligan

Re: [gmx-users] Replica Exchange MD using Gromacs

On 1/04/2011 6:52 PM, bsmith wrote: On 01/04/2011, at 6:29 PM, Mark Abraham wrote: On 1/04/2011 6:03 PM, Ruchi Gupta wrote: Dear gmx-users, I am facing some problems while running replica exchange MD using Gromacs. Few seconds after the job submission it ends with the following error mess

Re: [gmx-users] FW: protein split over boundary

Hello anahita, use pbc in your simulation. regards, Ravi   --- On Fri, 1/4/11, anahita wrote: From: anahita Subject: [gmx-users] FW: protein split over boundary To: "'Discussion list for GROMACS users'" Date: Friday, 1 April, 2

Re: [gmx-users] FW: protein split over boundary

ana johari wrote: dear user, Tanks for your advice, But the mdrun is know on the step of 33562880 but the protein was split at the first 1ns of MD. is it necessary to use “tpbconv” command and extract the *.tpr file just after first 1 ns and then use trjconv –ur compact a

Re: [gmx-users] The solvent group Water is not continuous

ahmet yıldırım wrote: Dear Justin, I have Fatal Errror:The solvent group Water is not continuous. I look at gmx-users mailing list search. I also have the same problem. You said:(http://lists.gromacs.org/pipermail/gmx-users/2010-January/048344.html) It is exactly what I said; you've proven

Re: [gmx-users] The solvent group Water is not continuous

On 1/04/2011 10:26 PM, ahmet yıldırım wrote: Dear Justin, I have Fatal Errror:The solvent group Water is not continuous. I look at gmx-users mailing list search. I also have the same problem. You said:(http://lists.gromacs.org/pipermail/gmx-users/2010-January/048344.html) It is exactly what I

Re: [gmx-users] The solvent group Water is not continuous

Dear Dr. Mark, I did you said but I have the same error. please look at attached file topol.top: [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 SOL 185 SOL 143 SOL 44125 TRS1 EDO1 01 Nis

Re: [gmx-users] The solvent group Water is not continuous

On 1/04/2011 11:03 PM, ahmet yıldırım wrote: Dear Dr. Mark, I did you said but I have the same error. please look at attached file topol.top: [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 SOL 185 SOL 143 SOL 44125 TRS

Re: [gmx-users] The solvent group Water is not continuous

I tried SOL 44453 but I still the same error 01 Nisan 2011 15:11 tarihinde Mark Abraham yazdı: > On 1/04/2011 11:03 PM, ahmet yıldırım wrote: > > Dear Dr. Mark, > > I did you said but I have the same error. please look at attached file > > topol.top: > > [ molecules ] > ; Compound#mols

Re: [gmx-users] The solvent group Water is not continuous

Is it a problem with an index file? is 'Water' an index group, and if so, is is contiguous. Erik ahmet yıldırım skrev 2011-04-01 14.15: I tried SOL 44453 but I still the same error 01 Nisan 2011 15:11 tarihinde Mark Abraham > yazdı: On 1/04/2011 11:03 PM,

Re: [gmx-users] The solvent group Water is not continuous

ahmet yıldırım wrote: I tried SOL 44453 but I still the same error Are you using some index file that is specifying a discontinuous water group? Have you properly re-created your genion input .tpr file from this new topology? -Justin 01 Nisan 2011 15:11 tarihinde Mark Abraham

Re: [gmx-users] The solvent group Water is not continuous

Dear users, I created nonaminoacid TRS.itp and EDO.itp files using ProDrg Beta. genion -s em.tpr -o solvated.gro -nname Na -nn 15 -g em.log select group:13 Fatal error: The solvent group SOL is not continuous: index[984]=5334, index[985]=5355 For more information and tips for troubleshooting, ple

Re: [gmx-users] The solvent group Water is not continuous

ahmet yıldırım wrote: Dear users, I created nonaminoacid TRS.itp and EDO.itp files using ProDrg Beta. ...and hopefully did a complete re-parameterization of the nonsense charges it gives. http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips That's an aside, completely unrelated

Re: [gmx-users] The solvent group Water is not continuous

When I created em.tpr I got the followings notes: *NOTE 1 [file topol.top, line 52]:* System has non-zero total charge: -1.50e+01 *NOTE 2 [file topol.top]:* The largest charge group contains 11 atoms. Since atoms only see each other when the centers of geometry of the charge groups the

Re: [gmx-users] The solvent group Water is not continuous

ahmet yıldırım wrote: When I created em.tpr I got the followings notes: *_NOTE 1 [file topol.top, line 52]:_* System has non-zero total charge: -1.50e+01 _*NOTE 2 [file topol.top]:*_ The largest charge group contains 11 atoms. Since atoms only see each other when the centers of geo

[gmx-users] Umbrella Sampling

1. how do you know that data is "not good"? It is not good science to remove data just because it doesn't match with your expected results. For now, there is no compelling reason to remove that data. 2. My first step in checking the convergence is to block average the time. If you have 10 n

[gmx-users] R: Re: adding a new residue in the ff

Dear Justin and Tsjerk, thank you very much for your last encouraging words...;-) I don't remember a time in my life where something that I needed, which was very complex to do, was already available...(apart from Gromacs package, of course!) About parameterization: sure I was intended to use the p

Re: [gmx-users] R: Re: adding a new residue in the ff

Anna Marabotti wrote: Dear Justin and Tsjerk, thank you very much for your last encouraging words...;-) I don't remember a time in my life where something that I needed, which was very complex to do, was already available...(apart from Gromacs package, of course!) About parameterization: sure I

[gmx-users] tpr file for trjconv command

Dear user, During simulation I restart the Md run and know I have two .tpr file. Because my molecule split over boundary after 1 ns of simulation,I want to use “trjconv” as a command to center my molecule but I don’t know to chose my first tpr file( for the first 1ns) or the second one after

[gmx-users] (no subject)

Dear Justin,Tsjerkand and Ravi, thanks from all of you for your kindness, I hop that I could use your recommend. anahita johari-- 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

Re: [gmx-users] tpr file for trjconv command

ana johari wrote: Dear user, During simulation I restart the Md run and know I have two .tpr file. Because my molecule split over boundary after 1 ns of simulation,I want to use “trjconv” as a command to center my molecule but I don’t know to chose my first tpr file( for the first 1ns) or t

[gmx-users] OPLS parametrizaton

Hi, I am trying to simulate mixtures of ethanol and trifluoroethanol and I would like to use the same parameters used on OPLS parametrization. On the OPLS1996 paper the authors starts by stating that they've used 267 molecules and "The box size varied from approximately 26 26  26 Å for met

[gmx-users] distance restraints for atoms on 2 chains

Hi, I have 5 chains in my Protein. I want to apply distance restraints for doing Umbrella Sampling for 2 atoms on different chains. Is there a way to do this since the two chains have separater itp files. Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listg

[gmx-users] Re: distance restraints for atoms on 2 chains

Also, the chains do not diffuse apart in time since they are position restrained(some parts of each chain are ...) On Fri, Apr 1, 2011 at 7:26 PM, Sai Pooja wrote: > Hi, > > I have 5 chains in my Protein. I want to apply distance restraints for > doing Umbrella Sampling for 2 atoms on different

Re: [gmx-users] Re: distance restraints for atoms on 2 chains

pdb2gmx -chainsep (-merge in 4.0.x and before) should allow you to create a merged [moleculetype] to apply distance restraints. If you're just trying to use a harmonic potential to define some sampling distance (for US), then distance restraints are not necessary, just apply the pull code.

Re: [gmx-users] OPLS parametrizaton

Marcelo Silva wrote: Hi, I am trying to simulate mixtures of ethanol and trifluoroethanol and I would like to use the same parameters used on OPLS parametrization. On the OPLS1996 paper the authors starts by stating that they've used 267 molecules and "The box size varied from approximatel

Re: [gmx-users] Re: distance restraints for atoms on 2 chains

The pull tutorial uses npt simulations.. is that required by the algorithm or can one use nvt after the system has been sufficiently equilibrated using npt? On Fri, Apr 1, 2011 at 7:32 PM, Justin A. Lemkul wrote: > > pdb2gmx -chainsep (-merge in 4.0.x and before) should allow you to create a > m

Re: [gmx-users] Re: distance restraints for atoms on 2 chains

Sai Pooja wrote: The pull tutorial uses npt simulations.. is that required by the algorithm or can one use nvt after the system has been sufficiently equilibrated using npt? Use whatever conditions are appropriate for your system. Tutorials should not be viewed as the only applicable con

[gmx-users] Precision mismatch

Hi Precision mismatch for state entry nosehoover-xi, code precision is double, file precision is float I am trying to extend an mdrun from a restart file. I get the error pasted above. The restart file was generated on a different cluster and I am now extending these simulations. Can this be reso

Re: [gmx-users] Precision mismatch

Sai Pooja wrote: Hi Precision mismatch for state entry nosehoover-xi, code precision is double, file precision is float I am trying to extend an mdrun from a restart file. I get the error pasted above. The restart file was generated on a different cluster and I am now extending these sim

Re: [gmx-users] Precision mismatch

On 02/04/11, Sai Pooja wrote: > Hi > >   > > Precision mismatch for state entry nosehoover-xi, code precision is double, > file precision is float > >   > > I am trying to extend an mdrun from a restart file. I get the error pasted > above. The restart file was generated on a different clus