[gmx-users] Discontinuity in first time-step velocities for diatomic molecule locally coupled to thermal drain

Good morning. While doing some verification, I tried to simulate a harmonically bound diatomic molecule where one of the atoms is coupled to a thermal reservoir held at zero Kelvin (a thermal "drain" or "sink"). The initial conditions were such that the atom coupled to the bath star

Re: [gmx-users] Re: pdb2gmx error

Dear Justin, Your suggestion of defining FVAL worked properly and at last I got the topology! :) Thanks a ooot! :) APPRECIATE YOU!   Sincerely, Shima - Original Message - From: Justin A. Lemkul To: Discussion list for GROMA

[gmx-users] Free energy between residues

Dear Gmx Users, I want to obtain the free energy difference between the pair of residues in my protein chain with respect to thheir distance. Would combinbation: 1) g_dist - distances between two groups during the simulation time 2) g_energy -fee (DelatG - with energy groups I am interested in s

Re: [gmx-users] NVT, NPT and then pulling?

Thank you Justin On Wed, Jun 27, 2012 at 9:36 PM, Justin A. Lemkul wrote: > > > On 6/27/12 4:30 PM, Steven Neumann wrote: >> >> Dear Gmx Users, >> >> I am wondering whether would you advise to run NVT, NPT (position >> restrained) and before the pulling simulation e.g of the ligand from >> protei

[gmx-users] chi1/chi2

during the simulation. I tried g_chi to obtain chi1 and chi2 values at the end I'm getting the plot withe values ranges from -180 to 180 . But in papers people have reported in 360 degree how can i get the data. Please give me suggestions -- View this message in context: http://gromacs.5086.n6

Re: [gmx-users] Free energy between residues

Dear Steven, Where are you working? >From my experience the g_energy -fee only gives a free enrgy estimate for the >whole system, so one has to pull out all the energy terms based on your index >file of interest and sum them in a spread sheet. if the -fee can do the >energy estimates for a s

Re: [gmx-users] Free energy between residues

On Thu, Jun 28, 2012 at 11:20 AM, lloyd riggs wrote: > Dear Steven, > > Where are you working? I work in UK, London. Why are you asking? > >From my experience the g_energy  -fee only gives a free enrgy estimate for > >the whole system, so one has to pull out all the energy terms based on your

Re: [gmx-users] Free energy between residues

On 6/28/12 6:33 AM, Steven Neumann wrote: On Thu, Jun 28, 2012 at 11:20 AM, lloyd riggs wrote: Dear Steven, Where are you working? I work in UK, London. Why are you asking? >From my experience the g_energy -fee only gives a free enrgy estimate for the whole system, so one has to pull

Re: [gmx-users] Free energy between residues

On Thu, Jun 28, 2012 at 11:42 AM, Justin A. Lemkul wrote: > > > On 6/28/12 6:33 AM, Steven Neumann wrote: >> >> On Thu, Jun 28, 2012 at 11:20 AM, lloyd riggs wrote: >>> >>> Dear Steven, >>> >>> Where are you working? >> >> >> I work in UK, London. Why are you asking? >> >> >>> >From my experience

[gmx-users] Justin's Paper

Hey Justin, J. Phys. Chem. B, 2010, 114 (4), pp 1652–1660 DOI: 10.1021/jp9110794 Publication Date (Web): January 7, 2010 I am wondering whether you calculated the free energy from windows obtained using different pulling rates (0.01, 0.005,. 0.001 nm/ps) ? Do you think you would get the same delt

Re: [gmx-users] Bootstrapping using g_wham

Hi, sorry for this late comment, I just stepped over this thread. Bootstrapping is indeed slow, because a complete WHAM analysis must be done for each bootstrap. I usually do much less bootstraps (around 50 to 100 gives a reasonable estimate), less bins, and I sometimes I reduce the tolerance

Re: [gmx-users] Force constant in g_wham

Hi, the umbrella potential is 0.5*k*(z-z0)^2 Jochen Am 6/14/12 11:41 PM, schrieb rainy908: Dear gmx-users, I am writing to clarify that the force constant kappa for g_wham corresponds to K_i itself, and not the quantity (1/2)*K_i in the umbrella potential W_i(ξ) = (K_i/2)*(ξ-ξ_i)^2. I rec

Re: [gmx-users] Justin's Paper

On 6/28/12 7:12 AM, Steven Neumann wrote: Hey Justin, J. Phys. Chem. B, 2010, 114 (4), pp 1652–1660 DOI: 10.1021/jp9110794 Publication Date (Web): January 7, 2010 I am wondering whether you calculated the free energy from windows obtained using different pulling rates (0.01, 0.005,. 0.001 nm/

Re: [gmx-users] Free energy between residues

On 6/28/12 6:51 AM, Steven Neumann wrote: On Thu, Jun 28, 2012 at 11:42 AM, Justin A. Lemkul wrote: On 6/28/12 6:33 AM, Steven Neumann wrote: On Thu, Jun 28, 2012 at 11:20 AM, lloyd riggs wrote: Dear Steven, Where are you working? I work in UK, London. Why are you asking? >From

[gmx-users] Fwd: Determine sec structure by MD

Hi Gromacs Friends,         I have the experimental result of change in Secondary structure of peptide from random coil to Beta sheet, as  the conc increases ( but  not know the Parallel or anti-parallel )                        I run Simulation of ( 30ns ) two peptide in random coil structure pu

[gmx-users] Problems with Dihedral transition times for dodecane

Daer all, I am trying to compute the transition times (TT) for all the angles in dodecane in the bulk (216) with gromacs 4.5.5 I have constructed an index file with all angles (C1C2C3C4C9C10C11C12) and for all the nine angles (C*C*C*C*) and use the following command for ea

[gmx-users] editbox removes dummy atoms

Hi everybody, I have an protein structure with many dummy atoms around it simulating the membrane around the protein. Those dummy atoms are signed in the file as an ATOM. When I want to put this protein with the membrane in a box with the command editconf -f 3m71.gro -o 3m71_box.gro -bt dodecahedr

Re: [gmx-users] editbox removes dummy atoms

On 6/28/12 10:11 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I have an protein structure with many dummy atoms around it simulating the membrane around the protein. Those dummy atoms are signed in the file as an ATOM. When I want to put this protein with the membrane i

[gmx-users] g_bar ... the right answer for the wrong reason?

Hi, i just performed a free energy TI calculation, to get the free energy of solvation of water in water (the chemical potential of water) i stuck closely to the templates given in the tutoral by justin lemkul. The final result i get with g_bar looks good, and the number is within the error-bars

Re: [gmx-users] editbox removes dummy atoms

I have found out that there was always the same residue number for all the dummy atoms. Perhaps that was the failure. Now I changed it so that they have all different residue numbers. But now I get the error: Atom N is used in an interaction of type improper in the topology database, but an atom o

Re: [gmx-users] g_bar ... the right answer for the wrong reason?

On 6/28/12 10:35 AM, Michael Brunsteiner wrote: Hi, i just performed a free energy TI calculation, to get the free energy of solvation of water in water (the chemical potential of water) i stuck closely to the templates given in the tutoral by justin lemkul. The final result i get with g_bar l

[gmx-users] RIMSP calculation

Hi Gromacs users I am trying to measure the similarity of the subspace sampled by a mutant protein-Ligand complex versus a wild type complex based on the eigen vectors computed using PCA. I was wondering, does and handy scripts does exists to compute the root mean square inner product ( RMSIP)

Re: [gmx-users] editbox removes dummy atoms

On 6/28/12 10:40 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: I have found out that there was always the same residue number for all the dummy atoms. Perhaps that was the failure. Now I changed it so that they have all different residue numbers. But now I get the error: Atom N is us

Re: [gmx-users] RIMSP calculation

Hi Vijayan, There must be a script somewhere in the archives (http://www.mail-archive.com/gmx-users@gromacs.org/msg02871.html) that calculates the RMSIP from the XPM file of eigenvector inner products. > I have come across many papers where they employ RMSIP to quantify the > similarity between P

Re: [gmx-users] g_bar ... the right answer for the wrong reason?

not all changes have been completed. g_bar_d -f mdv*.xvg -b 100; this is Program g_bar_d, VERSION 5.0-dev-20120628-b4320dc [...] WARNING: Some of these results violate the Second Law of Thermodynamics: This is can be the result of severe undersampling, or (more likely) the

Re: [gmx-users] RIMSP calculation

Hi Tsjerk Many thanks for your kind response. Got the script, will try to run it. Also thanks for clarifying RMSIP vs Cosine content values. Regards Vijayan.R On Thu, Jun 28, 2012 at 10:56 AM, Tsjerk Wassenaar wrote: > Hi Vijayan, > > There must be a script somewhere in the archives > (http://w

[gmx-users] segmentation fault-g_spatial

Dear D.M. I wrote g_spatial and Justin is correct that you simply need to use a larger number for -nab. It's not a "bug" per se, it is simply that I didn't write the program to do two loops through the input trajectory (one to determine the required bins and then allocate memory and then anoth

Re: [gmx-users] Free energy between residues

>>> I work in UK, London. Why are you asking? Because Im a super cop. No I just woundered about people with gmail, yahoo, or like mine gmx as to where they are at, etc... Ive been doing something similar, and it fits with whats expected, however what Justin said is true, without knowing what y

[gmx-users] Regarding umbrella sampling simulations along H-bonds

Dear Gromacs Users, I am simulating a system containing Protein-Mg-GTP complex. I intend to perform the umbrella sampling on the system to calculate PMF and to perform wham analysis. I have generated a series of conformations for the umbrella sampling. My main consideration is towards the 2 H-bon

[gmx-users] Can I set the dielectric constant for polymer and water separately

Dear users, I am simulating polymer in water and get water density lower than experimental one at 363K, 1bar. The water model I use is spce.Gromacs version 4.5.4. Can it be caused by setting dielectric constant epsilon_r = 3.6, which is the value of polymer and much smaller than that of water? I

[gmx-users] Berger lipid

Hi all, I want to simulate a protein in POPC bilayer by CHARMM27 FF. I know phospholipids and protein are defined well in CHARMM27. Is Berger lipid required ?   Thanks for your replies in advance. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailm

Re: [gmx-users] Berger lipid

On 6/28/12 8:15 PM, Shima Arasteh wrote: Hi all, I want to simulate a protein in POPC bilayer by CHARMM27 FF. I know phospholipids and protein are defined well in CHARMM27. Is Berger lipid required ? No, these are different force fields entirely. The CHARMM36 parameter set is better for

Re: [gmx-users] Berger lipid

Thanks. Yes, you told me this before CHARMM36 is better than CHARMM27. But I'm afraid of using  C36. Because I think it's a newer FF and and less studies have done by it. Then if I face a problem, I can't find a way through articles!  Don't you think so?   Sincerely, Shima - Original Mess

Re: [gmx-users] Berger lipid

On 6/28/12 8:23 PM, Shima Arasteh wrote: Thanks. Yes, you told me this before CHARMM36 is better than CHARMM27. But I'm afraid of using C36. Because I think it's a newer FF and and less studies have done by it. Then if I face a problem, I can't find a way through articles! Don't you think s

Re: [gmx-users] Berger lipid

  Yes, I have studied the article by Jeffery B. Klauda and other articles related to C36. And know where the parameters of CHARMM36 were derived. By the way, when I search the lipidbook to find the .itp file I can't find it! What about the lipid .itp ? Is it required yet? ( in your tutorial it

Re: [gmx-users] Berger lipid

On 6/28/12 8:43 PM, Shima Arasteh wrote: Yes, I have studied the article by Jeffery B. Klauda and other articles related to C36. And know where the parameters of CHARMM36 were derived. By the way, when I search the lipidbook to find the .itp file I can't find it! What about the lipid .itp

Re: [gmx-users] Berger lipid

Yes, I know that as studied the Kalp15 tutorial. Sorry, the last question :)  :   DO I need to run pdb2gmx to get the top file of POPC in CHARMM36? Is it ok?  Because I see that POPC.itp is also required for simulation of protein in bilayer. Again, thanks   Sincerely, Shima - Original Me

Re: [gmx-users] Berger lipid

On 6/28/12 8:54 PM, Shima Arasteh wrote: Yes, I know that as studied the Kalp15 tutorial. Sorry, the last question :) : DO I need to run pdb2gmx to get the top file of POPC in CHARMM36? Is it ok? Because I see that POPC.itp is also required for simulation of protein in bilayer. You ne

[gmx-users] Regarding umbrella sampling simulations along H-bonds

Dear Neeru: Please reformulate your question so that it is clear what you are asking. If your question is "how do I do US?" you are unlikely to get much help here beyond being directed to one of the US tutorials that you can find by a google search. If however, you know how to do US but have a

RE: [gmx-users] Berger lipid

Uh didn't we go through all of this like more than a month ago? I published a paper using C36 POPC and even a linked to my popc.itp for it on this list... Of course Shima is welcome to pdb2gmx his own POPC, which I am fairly certain will result in an identical file... Lipidbook seems to only ha

[gmx-users] Berger lipid

I am sure that a lot of this could be avoided if the gromacs users-list search feature worked. Every search that I do returns ten to one hundred versions of each hit, making it nearly unusable. Google is ok, but it doesn't search the gromacs list nearly as well as the old specific search on the

Re: [gmx-users] Berger lipid

Yes, I remember now...you are right :) But I didn't know the linked you sent me, was your own output! However  I wanted to know if it is necessary to produce the .itp file on my own or not. I still have this link, so will cite to you. It would be a good idea to see its package i

Re: [gmx-users] Berger lipid

Dear Peter, Is this article is the one you talked about? Beyond Modeling: All-Atom Olfactory Receptor Model Simulations Thanks in advance   Sincerely, Shima - Original Message - From: Peter Lai To: Discussion list for GROMACS users Cc: Sent: Friday, June 29, 2012 7:14 AM Subject: RE:

[gmx-users] popc36 + paper

Dear Peter, Is this article is the one you talked about? "Beyond Modeling: All-Atom Olfactory Receptor Model Simulations" Thanks in advance   Sincerely, Shima   Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain t