[gmx-users] Assignment of new velocities for multi-runs

Dear All! I'd like to perform several simulations of the membrane protein started from the common conditions which differs only in the initial velocities ( for each simulation random speed distribution will be used from the Maxwell distribution). Because I simulate membrane protein the long equil

Re: [gmx-users] Re: Notes and warnings using grompp

On 9/28/12 5:13 PM, Sonia Aguilera wrote: Hi, I understand that usually it is needed to add counterions . I´m performing a free energy calculation and I want to see the free energy change without adding the ions. What I´m asking is why the program reads a total charge of -13.02 not 13.0. T

[gmx-users] Re: Notes and warnings using grompp

Hi, I understand that usually it is needed to add counterions . I´m performing a free energy calculation and I want to see the free energy change without adding the ions. What I´m asking is why the program reads a total charge of -13.02 not 13.0. The note says that it must be an integer, but

[gmx-users] Notes and warnings using grompp

Hi, I´m getting the following notes when using grompp to generate the tpr file. My system is a protein in water. I already checked the topology file and the sum of my charges are -13. Should I ignore it? Why is it assuming that value? NOTE 1 [file OmpC.top, line 23461]: System has non-zero to

Re: [gmx-users] Notes and warnings using grompp

On 9/28/12 4:10 PM, Sonia Milena Aguilera Segura wrote: Hi, I´m getting the following notes when using grompp to generate the tpr file. My system is a protein in water. I already checked the topology file and the sum of my charges are -13. Should I ignore it? Why is it assuming that value?

[gmx-users] Notes and warnings using grompp

Hi, I´m getting the following notes when using grompp to generate the tpr file. My system is a protein in water. I already checked the topology file and the sum of my charges are -13. Should I ignore it? Why is it assuming that value? NOTE 1 [file OmpC.top, line 23461]: System has non-zero to

Re: [gmx-users] Re: distance restraint

On 9/28/12 3:34 PM, pauladelgado wrote: This is the distance of one pair of atoms that i restraint. I apologize if i did't mention why i am using distance restraint, i am working with a protein obtained using homology modelling,

[gmx-users] Re: distance restraint

This is the distance of one pair of atoms that i restraint. I apologize if i did't mention why i am using distance restraint, i am working with a protein obtained using homology modelling, the next step after i get the protein str

Re: [gmx-users] mails of other users in this mailing list

On 9/28/12 3:07 PM, Lara Bunte wrote: Hello Is there a way to get all mails from the GROMACS mailing list for a special email adress? To be more precisely I want to have all messages that are asked and answered for a special user. This is motivated out of the fact that I saw that I am not

[gmx-users] mails of other users in this mailing list

Hello Is there a way to get all mails from the GROMACS mailing list for a special email adress? To be more precisely I want to have all messages that are asked and answered for a special user. This is motivated out of the fact that I saw that I am not alone with my system. There are other peo

Re: [gmx-users] Umbrella sampling-protein-ligand complex

On 9/28/12 2:19 PM, Archana Sonawani wrote: Dear Justin, So do I have to carry out umbrella sampling simulations separately for the three complexes or put the three ligands together with the protein and pull the ligands one by one to calculate the binding energy. I am confused. Each complex

Re: [gmx-users] Umbrella sampling-protein-ligand complex

Dear Justin, So do I have to carry out umbrella sampling simulations separately for the three complexes or put the three ligands together with the protein and pull the ligands one by one to calculate the binding energy. I am confused. Thanks in advance. Regards, Archana On Fri, Sep 28, 2012 at

Re: [gmx-users] Re:provide opt way to perform simulation for protein and peptide -reg

On 9/28/12 1:03 PM, venkatesh s wrote: Respected gromacs Users, I want perform protein (only one chain) + peptide (five amino acid) simulation to understand interaction between both (can say what role are playing peptide with protein ) so i did like this p

Re: [gmx-users] something wrong with BlueGene/P

Hi Kai, I would suggest running (Berendsen) NpT equilibration with a large tau_p, followed by a few cycles in which you lower tau_p. Hope it helps, Tsjerk On Sep 28, 2012 2:53 PM, "Matthew Zwier" wrote: Hi Kai, A system that is marginally stable frequently succeeds in propagating on one mach

Re: [gmx-users] Re: distance restraint

On 9/28/12 12:53 PM, pauladelgado wrote: Yes i found this document "Computer simulations: Orientation of Lysozyme in vacuum under the influence of an electric field" where i found about the conditions i mentioned before for vacuum simulations. So what should i do? You've been asking about im

[gmx-users] Re: distance restraint

Yes i found this document "Computer simulations: Orientation of Lysozyme in vacuum under the influence of an electric field" where i found about the conditions i mentioned before for vacuum simulations. So what should i do? -- View this message in context: http://gromacs.5086.n6.nabble.com/dist

Re: [gmx-users] Re: distance restraint

On 9/28/12 12:25 PM, pauladelgado wrote: Other thing is that i couldn't found a lot of literature about the conditions for vacuum simulations, can you help me with this please, Thanks a lot Justin Searching Google Scholar for "protein vacuum simulations" (without quotes) turns up 38000 resu

[gmx-users] Re: distance restraint

Other thing is that i couldn't found a lot of literature about the conditions for vacuum simulations, can you help me with this please, Thanks a lot Justin Paula Here is the graph of energy of distance restraint -- View this m

Re: [gmx-users] Re: distance restraint

On 9/28/12 12:18 PM, pauladelgado wrote: The distance restraint energy is arrond 13700 KJ/mol, is that ok?, but whta happend with mi resulting pdb, i can't appreciate the distance restraint s i made. No, that's not OK. The very large value of energy suggests that the desired distances are

[gmx-users] Re: distance restraint

The distance restraint energy is arrond 13700 KJ/mol, is that ok?, but whta happend with mi resulting pdb, i can't appreciate the distance restraint s i made. With respect to vacuum simulation, i am doing energy minimization and md with no periodic boundaries, with coulombtype=Cutt-off and the cut

Re: [gmx-users] provide opt way to perform simulation for protein and peptide -reg

On 9/28/12 10:07 AM, venkatesh s wrote: Respected gromacs Users, i want perform stimulation for protein + peptide (in water medium only not membrane protein) 1. Can i use the Docked conformation (better conformation both protein + peptide make it as one

Re: [gmx-users] Umbrella sampling-protein-ligand complex

On 9/28/12 9:27 AM, Archana Sonawani wrote: Hi, I have performed simulations for 3 different ligands complexed with the same protein. I want to compare the binding energies of these different three complexes. Will umbrella sampling be useful in this case? Several methods could be used, and

Re: [gmx-users] g_hbond

On 9/28/12 8:53 AM, Gavin Melaugh wrote: Hi I have an alcohol system and I want to calculate the number of H bonds during the trajectory. My atom type labels are C2-C2-C2-CO-OH-HO. CO denotes carbon bonded to oxygen, OH denotes alcohol oxygen, and HO denotes alcohol hydrogen. In g_hbond how d

[gmx-users] g_hbond

Hi I have an alcohol system and I want to calculate the number of H bonds during the trajectory. My atom type labels are C2-C2-C2-CO-OH-HO. CO denotes carbon bonded to oxygen, OH denotes alcohol oxygen, and HO denotes alcohol hydrogen. In g_hbond how do I specify my groups to consider for H bondi

Re: [gmx-users] something wrong with BlueGene/P

Hi Kai, A system that is marginally stable frequently succeeds in propagating on one machine and fails on another. I've observed this even between Xeon and Opteron systems, which is fairly minor architectural difference. Since your system works in NVT but not NPT, this would seem to imply that th

Re: [gmx-users] Re: distance restraint

On 9/27/12 7:07 PM, pauladelgado wrote: *file alfadrest.itp* [ distance_restraints ] ; i j ? label funct loup1up2 weight 8002 10641 1 0 10.40.50.6 1 8040 10616 1 0 10.40.5

Re: [gmx-users] tau_t and tc_grps for v-rescale (2)

On 9/28/12 3:18 AM, Felipe Pineda, PhD wrote: Hi again, I posted yesterday the query below, but have not received any feedback up to now. I would like to put my question in another way: in Justin's "CAP-15 in DPPC" tutorial he uses during NVT equilibration Bussi's thermostat (V-rescale) togeth

Re: [gmx-users] doubt in minimization part

On 9/28/12 4:25 AM, Shine A wrote: Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. Now I am confusing with the following ( shown at botom) part of the tutorial.Here minimization means to minimize system_inflated.gro, is it right? Then without .epr and .top files

Re: [gmx-users] g_tcaf segmentation fault

I check my .mdp setting and you were right. I haven't been saving the velocities in my .trr file. I change my setting and everything worked fine. Thanks for your help Stelios On 09/27/2012 03:37 PM, Tsjerk Wassenaar wrote: Re: [gmx-users] g_tcaf segmentation fault The .trr file can contain c

[gmx-users] Exclusions in TIP4P

Hi all, In the OPLS-AA tip4p.itp file I see: [ moleculetype ] ; molname nrexcl SOL 2 and [ exclusions ] 1 2 3 4 2 1 3 4 3 1 2 4 4 1 2 3 If bonded interactions are included (FLEXIBLE define

[gmx-users] doubt in minimization part

Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. Now I am confusing with the following ( shown at botom) part of the tutorial.Here minimization means to minimize system_inflated.gro, is it right? Then without .epr and .top files of system_inflated.gro how can I do thi

[gmx-users] tau_t and tc_grps for v-rescale (2)

Hi again, I posted yesterday the query below, but have not received any feedback up to now. I would like to put my question in another way: in Justin's "CAP-15 in DPPC" tutorial he uses during NVT equilibration Bussi's thermostat (V-rescale) together with three separate coupling groups: ; Te