Re: [gmx-users] Free energy change with harmonic restraints
Dear Natalie,
The weekend was good. Thanks. I hope that you have a great weekend too.
If you manage to simulate the system with restraints (A) and without
restraints (B) you can calculate the free energy difference between
A/B to a system in which the ligand is not interacting with the
environment (protein and solvent) at all. The free energy associated
with the restraints when the ligand is not interacting via VDW and
electrostatic interactions with the environment can be calculated with
the analytic expressions.
In summary you can calculate Delta F_{A->A'} and F_{B->B'} where A'
and B' are when the ligand is not interacting via VDW and
electrostatic interactions with the environment without and with
restraints respectively. This can be calculated by TI, Bar etc. Then
there is to calculate F_{B'->B''} where this free energy difference is
given by the analytic equations. F_B''=F_A' since it's a system in
which the ligand is not interacting with the environment (protein and
solvent) at all. Thus you can calculate F_{A->A'} and F_{B->B''} and
obtain F_{A->B}.
I hope it helps.
Best regards,
Asaf
Quoting Natalie Nguyen :
Dear Asaf,
I hope you have had a great weekend!
I have tried applying TI with restraint-lambdas to measure the free
energy difference of applying restraints without success (no dhdl
files were being outputted). The tutorial in the link provided by
Hannes Loeffler I have looked over before, but my intentions are not
measuring the free energy change of binding.
I would like to know in more detail on how to approach this.
Much appreciated,
Natalie
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of
asaffa...@post.tau.ac.il
Sent: Thursday, July 09, 2015 5:58 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Free energy change with harmonic restraints
Dear Natalie,
What I can say is that e.g Thermodynamic Integration should give the
free energy difference of this transformation. If you are interested
in the free energy of binding the link provided to you by Hannes
Loeffler may be useful. Also, for such a k value in case you will need
analytic equations it will be better to use the exact equations (the
equations in this link are approximate). I'll supply an exact equation
if you'll need for the free energy of a dihedral harmonic term.
I hope to have more time next week and give more details (the weekend
starts here).
Best regards,
Asaf
I hope to have more time next week and to try
Quoting Natalie Nguyen :
Dear Asaf,
Thank you again for putting in the time to respond to me so quickly.
What I have been trying to do was start from a system that is not
restrained and grow the restraints onto the ligand, measuring the
change in free energy of this. The harmonic restraints used are that
of the umbrella pull code with a force constant of k= 1000
kJ/mol*nm^2. It is mentioned In the Gromacs manual for mdp options
that the pull code can be controlled with "restraint-lambdas", but
there is not much detail other than this. I imagine that lambda =0
would represent a nonexistent potential with k= 0 and at lambda = 1
a full strength potential would be imposed.
Please feel free to ask me to add more detail!
Warm regards,
Natalie
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of
asaffa...@post.tau.ac.il
Sent: Thursday, July 09, 2015 10:38 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Free energy change with harmonic restraints
Dear Natalie,
You are welcome.
Could you please explain in more detail so maybe I can help?
Do you want to change the strength of the restraints and measure the
free energy difference associated with this change?
Thanks. p.s there is also http://arxiv.org/pdf/1307.1620v7.pdf with
the same equations.
Best regards,
Asaf
Quoting Natalie Nguyen :
Dear Asaf,
Thank you for the quick reply!
I was wondering if it was possible to use thermodynamic integration
to represent growing harmonic restraints aside from using an
analytical method.
I will cite this article most definitely!
Natalie Nguyen
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of
asaffa...@post.tau.ac.il
Sent: Thursday, July 09, 2015 7:45 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Free energy change with harmonic restraints
Dear Natalie,
You have in
http://xxx.tau.ac.il/pdf/1502.07196v3.pdf
exact free energy of harmonic covalent bond and bond angle terms (or
restrains). See Eqs. (2) and (3).
There are also previous studies in the references there.
For the dihedral term I assume it can also be calculated exactly (I
might upload it).
There is also to think if there are other contributions.
If you are using it please cite.
Best regards,
Asaf
Quoting Natalie Nguyen :
Dear all,
I am tryin
[gmx-users] H-bonding autocorrelation function
Hi,
I have a question about the H-bonding autocorrelation function, if I have
a trajectory, say
1-1-1-1-1-1-0-1 (1 is H-bonding, 0 is no H-bonding), the time step is
0.006 ps, the correlation is equal to / , my answer
is
at t = 0.006, correlation = 7/7 = 1;
at t = 0.012, correlation = 5/7 = 0.714;
at t = 0.018, correlation = 5/7 = 0.714;
at t = 0.024, correlation = 4/7 = 0.571;
at t = 0.03, correlation = 3/7 = 0.429;
at t = 0.036, correlation = 2/7. = 0.286,
at t = 0.042, correlation = 1./7. = 0.143,
at t = 0.048, correlation = 1./7. = 0.143,
at t = 0.054, correlation = 0.
However, when i check gromacs, I found it gives a different answer, here
is the command I use "g_hbond -s md.tpr -f new.gro -ac -dist -temp 400 -b
72.444 -e 72.486 -dt 0.006", it uses only the time between 72.444 and
72.486 ps with a timestep of 0.006 ps, and the following is the h-bond
number file obtained from gromacs,
time (ps) H-bond ( H-bond without angle requirement)
72.444 1 1
72.451 1
72.456 1 1
72.462 1 1
72.468 1 1
72.474 1 1
72.480 2
72.486 1 1
and the hbac gives ,
time (ps)C(t)
0 1
0.0059967 0.97
0.012001 0.93
the following is from hbac.xvg,
@ s0 legend "Ac\sfin sys\v{}\z{}(t)"
@ s1 legend "Ac(t)"
@ s2 legend "Cc\scontact,hb\v{}\z{}(t)"
@ s3 legend "-dAc\sfs\v{}\z{}/dt"
0 1 1 0 235.274
0.00599670.4117640.97 -9.93411e-09 117.637
0.012001 -0.4117640.930.17 -0
Am my calculation wrong? Can anyone help me to resolve this? Thanks!
Thanks!
Fangyong
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Re: [gmx-users] Adding missing heavy atoms
On 7/11/15 1:03 AM, prasun kumar wrote: Dear All I have generated the base atoms of nucleotides in a structure, but it does not have sugar and phosphate atoms. Is there any method by which I can add them appropriately (either in A or B form) If you already have the base configuration, you cannot choose between A- and B-form helices; the stacking of each is different. I suggest NAB from AmberTools. It is extremely is easy to use for generating structures of any geometry and sequence. http://ambermd.org/tutorials/basic/tutorial1/section2.htm -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging --> segmentation fault)
On 7/10/15 7:21 PM, Justin Lemkul wrote: On 7/10/15 7:15 PM, Nathan K Houtz wrote: Actually, I think I found the problem. When i looked at the pdb files in vmd the first time I missed it, but a colleague had a hunch and I found that he was right! I think that shake is constraining atoms to the wrong molecules. Here's a screenshot I took where you can see what I mean:http://imgur.com/1bgThDv Sorry, this doesn't make sense to me. Constraints are applied per-moleculetype; they cannot be applied between molecules. I can't tell anything from this image. I'm still not sure how to fix it though. The molecule numbering in my .gro file is correct, and there are only 4 atoms per molecule (or 3 plus the dummy). How can I tell shake to look at each molecule individually? Or have I made a mistake somewhere? Here are my most recent files: .gro file: (only part of it -- there is a character limit. this is the first and last ten molecules with the box dimensions at the bottom) http://textuploader.com/e898 topology file: http://textuploader.com/e89g minimization: http://textuploader.com/e8rc .mdp file: http://textuploader.com/e896 One final thing after I took another look on a hunch - constraining all angles is very unstable, and doing it with SHAKE is (I think) even worse. You've got [constraints] manually defined in the topology to keep the geometry rigid; you should set "constraints = none" to just use those constraints specified in the topology. -Justin log file from a failed simulation: http://textuploader.com/e80y Thanks for your help! If you do still want the full .gro file to run the simulation, I can look for a different file host. I really would like a nice tarball with everything so that I can play with it a bit. That's the only way I'm going to have any chance of figuring it out. I would also dispute your previous assertion that the temperature is fine - it goes out of control immediately :) -Justin Nathan - Original Message - From: "Justin Lemkul" To: gmx-us...@gromacs.org Sent: Friday, July 10, 2015 5:06:34 PM Subject: Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging --> segmentation fault) On 7/9/15 9:23 PM, Nathan K Houtz wrote: Thanks for your explanations, Dr. Lemkul. I had already corrected a couple of the things you suggested. Gromacs won't actually let me run with Nose-Hoover and Parrinello-Rahman together (or at least, it gives a warning not to do that and stops). I'd like to run in NVT anyway, so I had set Pcoupl to 'no'. I had also increased the cutoffs and my nstlist is 20. I have now also changed the tcoupl to v-rescale, but unfortunately that alone didn't help. So I'm not sure exactly what I can inspect to find the source of my error. I know that temperature, pressure, and total energy are all warning signs of bad things if they misbehave, but they were all fairly constant throughout the simulation. (This is for the flexible-model simulation:) The starting energy for 1700 water molecules at 120K was -1.08744e+05, and it finished at -1.06047e+05 with no significant variations on any step. Pressure and temperature were also fine. I attempted to look at the results visually in vmd but I might have done something wrong because the .trr file has some error in it and vmd crashes. But the starting geometry after minimization looks fine: none of the molecules were moved out of their position in the crystal. For the constrained molecules, the energy stays about the same (about -1e+5) for the first 8 timesteps and then quickly blows up to +2e15 at step 12 before it obviously fails. I get shake warnings from step 0 though. In vmd, the first 8 steps look reasonable (checking the .pdb files that gromacs outputs when there are warnings) and all the molecules seem to hold their places in the crystal, but then at step 9 suddenly some of the molecules become misshapen with very long or very short bonds. Of course it goes downhill from there, but I can't figure out what's causing the problems since it's clearly happening from the very beginning (according to the shake warnings). What other things could I look at to troubleshoot my problem? Not sure, but at least the failure happens fast. Upload all your input files somewhere and I'll take a few minutes to see if I can spot anything. -Justin Thanks for your help, Nathan - Original Message - From: "Justin Lemkul" To: gmx-us...@gromacs.org Sent: Thursday, July 9, 2015 7:39:47 AM Subject: Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging --> segmentation fault) On 7/8/15 8:06 PM, Nathan K Houtz wrote: Hello, I deleted the email and can't respond to my last reply directly - sorry! I got this response from Mark Abraham: Hi, Try doing some EM and initial equilibration with no constraints at all, perhaps? Mark I tried commenting out the shake commands, and got a short (5000 step) simulation to run just fine without
Re: [gmx-users] question
And now I have a reference for when I tell people that PRODRG is utterly useless. Thank you. JL> On 7/11/15 3:43 AM, Atila Petrosian wrote: >> Dear Mark, >> >> Thanks for your attention, >> >> If I want to use PRODRG server and not ATB for my ligand, how to modify >> charge and charge group number? >> >> I am beginner in this acse, please guide about that. >> JL> Shameless self-promotion for the millionth time: JL> http://pubs.acs.org/doi/abs/10.1021/ci100335w JL> -Justin JL> -- JL> == JL> Justin A. Lemkul, Ph.D. JL> Ruth L. Kirschstein NRSA Postdoctoral Fellow JL> Department of Pharmaceutical Sciences JL> School of Pharmacy JL> Health Sciences Facility II, Room 629 JL> University of Maryland, Baltimore JL> 20 Penn St. JL> Baltimore, MD 21201 JL> jalem...@outerbanks.umaryland.edu | (410) 706-7441 JL> http://mackerell.umaryland.edu/~jalemkul JL> == -- Best regards, Alexmailto:nedoma...@gmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging --> segmentation fault)
On 7/10/15 7:15 PM, Nathan K Houtz wrote: Actually, I think I found the problem. When i looked at the pdb files in vmd the first time I missed it, but a colleague had a hunch and I found that he was right! I think that shake is constraining atoms to the wrong molecules. Here's a screenshot I took where you can see what I mean:http://imgur.com/1bgThDv Sorry, this doesn't make sense to me. Constraints are applied per-moleculetype; they cannot be applied between molecules. I can't tell anything from this image. I'm still not sure how to fix it though. The molecule numbering in my .gro file is correct, and there are only 4 atoms per molecule (or 3 plus the dummy). How can I tell shake to look at each molecule individually? Or have I made a mistake somewhere? Here are my most recent files: .gro file: (only part of it -- there is a character limit. this is the first and last ten molecules with the box dimensions at the bottom) http://textuploader.com/e898 topology file: http://textuploader.com/e89g minimization: http://textuploader.com/e8rc .mdp file: http://textuploader.com/e896 log file from a failed simulation: http://textuploader.com/e80y Thanks for your help! If you do still want the full .gro file to run the simulation, I can look for a different file host. I really would like a nice tarball with everything so that I can play with it a bit. That's the only way I'm going to have any chance of figuring it out. I would also dispute your previous assertion that the temperature is fine - it goes out of control immediately :) -Justin Nathan - Original Message - From: "Justin Lemkul" To: gmx-us...@gromacs.org Sent: Friday, July 10, 2015 5:06:34 PM Subject: Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging --> segmentation fault) On 7/9/15 9:23 PM, Nathan K Houtz wrote: Thanks for your explanations, Dr. Lemkul. I had already corrected a couple of the things you suggested. Gromacs won't actually let me run with Nose-Hoover and Parrinello-Rahman together (or at least, it gives a warning not to do that and stops). I'd like to run in NVT anyway, so I had set Pcoupl to 'no'. I had also increased the cutoffs and my nstlist is 20. I have now also changed the tcoupl to v-rescale, but unfortunately that alone didn't help. So I'm not sure exactly what I can inspect to find the source of my error. I know that temperature, pressure, and total energy are all warning signs of bad things if they misbehave, but they were all fairly constant throughout the simulation. (This is for the flexible-model simulation:) The starting energy for 1700 water molecules at 120K was -1.08744e+05, and it finished at -1.06047e+05 with no significant variations on any step. Pressure and temperature were also fine. I attempted to look at the results visually in vmd but I might have done something wrong because the .trr file has some error in it and vmd crashes. But the starting geometry after minimization looks fine: none of the molecules were moved out of their position in the crystal. For the constrained molecules, the energy stays about the same (about -1e+5) for the first 8 timesteps and then quickly blows up to +2e15 at step 12 before it obviously fails. I get shake warnings from step 0 though. In vmd, the first 8 steps look reasonable (checking the .pdb files that gromacs outputs when there are warnings) and all the molecules seem to hold their places in the crystal, but then at step 9 suddenly some of the molecules become misshapen with very long or very short bonds. Of course it goes downhill from there, but I can't figure out what's causing the problems since it's clearly happening from the very beginning (according to the shake warnings). What other things could I look at to troubleshoot my problem? Not sure, but at least the failure happens fast. Upload all your input files somewhere and I'll take a few minutes to see if I can spot anything. -Justin Thanks for your help, Nathan - Original Message - From: "Justin Lemkul" To: gmx-us...@gromacs.org Sent: Thursday, July 9, 2015 7:39:47 AM Subject: Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging --> segmentation fault) On 7/8/15 8:06 PM, Nathan K Houtz wrote: Hello, I deleted the email and can't respond to my last reply directly - sorry! I got this response from Mark Abraham: Hi, Try doing some EM and initial equilibration with no constraints at all, perhaps? Mark I tried commenting out the shake commands, and got a short (5000 step) simulation to run just fine without blowing up. Before, I would get shake warnings from the first few steps and a segmentation fault around step 13 or 14. I would like to be able to simulate with rigid molecules, though. Why would the simulation work with flexible molecules but not rigid ones? Flexible water allows weird geometry, which is probably coming up and causing your constr
Re: [gmx-users] RB dihedral type in amber99sb-ildn ffbonded.itp
On 7/11/15 2:21 AM, tarak karmakar wrote: Dear All, I need to impose a distance restraints between COM of protein active site residues and COM of a ligand. But the problem is I am using an .itp file generated from acpype. While I use the ligand.itp externally, I can not impose the distance restraints between the protein and the ligand. Then, I Don't use distance restraints. Use the pull code. That's what it is for. tried to include (merge) the parameters of the ligand to specific files present in the amber99sb-ildn directory. I tried the following, atomtypes.atp => atomtypes (gaff) of the ligand molecule are appended. aminoacids.rtp => generated a new .rtp entry for the ligand molecule, ffnonbonded.itp => non-bonded parameters are appended ffbonded.itp => copied and pasted the bond, angle parameters, and RB dihedrals Merging this information should not be necessary. Simply adding the new parameters in the ligand's .itp file should take care of everything, provided it is #included in the proper sequence. -Justin Now, the problem I am facing with the dihedral, the implementations of RB type (type 3) and proper dihedral type 9. It seems pdb2gmx does not read the dihedrals specified in the ffbonded.itp for the ligand molecule. There are clues from old posts, https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-May/097280.html https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-April/080306.html Include the dihedral parameters after the [ bonds ] section in the .rtp file like, [ dihedrals ] C1' C2' C3' C4' 33.68192 3.09616 -2.09200 -3.01248 0.0 0.0 C1' C2' C3' O3' 30.65084 1.95253 0.0 -2.60338 0.0 0.0 C1' C2' C3' H3' 30.65084 1.95253 0.0 -2.60338 0.0 0.0 C1' C2' O2' HO2 31.71544 0.96232 0.0 -2.67776 0.0 0.0 In this case, I have deleted the dihedral parameters in the ffbonded.itp file. However, it does not seem to solve the problem. :( Would you like to suggest me something related to this? Thanks, Tarak -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] question
On 7/11/15 3:43 AM, Atila Petrosian wrote: Dear Mark, Thanks for your attention, If I want to use PRODRG server and not ATB for my ligand, how to modify charge and charge group number? I am beginner in this acse, please guide about that. Shameless self-promotion for the millionth time: http://pubs.acs.org/doi/abs/10.1021/ci100335w -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Simulation with ligand on protein surface
On 7/11/15 2:51 AM, adam zalewski wrote: Hi Justin and sorry for the vagueness What I'm observing are displacements from the binding site (granted, they are quite shallow) and loss of any relation to the experimental data. They also happen fairly fast (often below 10ns) and just looking at the trajectory, makes me think something is wrong (e.g. a nicely buried phenyl ring being exposed into the solvent). Now that you mention it, the ligand parametrization does seem like the place to look. Any hints regarding that (acpype/antechamber or otherwise) ? AMBER parametrization is done relative to QM target data, e.g. RESP fitting. If your phenyl ring is flipping into the solvent, is is probably overly polar. Compare its charges against something like Phe. If the charges are dissimilar, you'll have to do a more thorough parametrization of the molecule by targeting QM data in the manner prescribed by the force field (and there's lots of literature on that). -Justin Thanks and a nice weekend, Adam On 07/10/2015 11:09 PM, Justin Lemkul wrote: On 7/10/15 5:02 AM, az wrote: Hi all I was wondering if anyone had experience/pointers regarding simulating protein-ligand systems where the interface was heavily surface-exposed ? I've been running quite a few of those these days with Amber99SB--ildn, TIP3P, and acpype (i.e. Ambertools) for ligand parametrization, mainly for the purpose of probing stability of peptidomimetic docking poses (10-50ns; aside from the force-field I follow Justin Lemkul's tutorial quite closely). Having however noticed that some of my reference ligands (i.e. ones with crystallographic/NMR data) wander away from where they should remain, I started wondering whether there could be something wrong with my setup. I obviously understand there's a zillion possibilities here, but I was still wondering whether there exists some sort of 'good-practice' for such cases (e.g. choice of force-fields, equilibration protocols ... anything really). I cannot be the only one doing this and if anyone has a protocol that served them well in the past, I'd love to learn about it. In general, if an interaction is not preserved, that suggests a poor parametrization of that ligand. But "wander away" is a bit vague; if it's just a small reorientation or something, it may not actually be "wrong" at all. Depends on the quality of the experimental data and the agreement with experimental conditions, as well. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on VMD analysis of the gromacs production MD
Dear All, After energy minimization, 100 ps NVT md and 100 ps NPT md (based on the on-line lysozyme tutorial), I have processed a 30 ns production MD (also based on the on-line lysozyme tutorial). Then I load the NPT.gro and the 30ns_production_md.xtc to the VMD, and by VMD I find in the whole 30 ns md, the whole protein molecule has an about 50 degree rotation (the 50 degree occurs gradually in the 15 ns md, not a sudden 50 degree rotation). Is this 50 degree rotation normal or abnormal? If by VMD I want to observe the local conformation changes in the whole 30 ns md, rather than the global 50 degree rotation, will you please tell me which trajectory file I need to load to VMD, and by which command I can get that trajectory file? Best regards. Smith -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Reaching the desired pressure and density
Hi, Dear users,I have created a box of polymer with about 50 molecules. I'm performing NPT runs to reach to the pressure of 1 bar. After a long time of simulation (15 ns) the average pressure is still about -0.5 and the density has saturated to around 700 kg/m^3 which should become 1200 kg/m^3 at the pressure of one bar. These are the related parameters in .mdp file: ; Pressure coupling is onpcoupl = berendsen ; Pressure coupling on in NPTpcoupltype = isotropic ; uniform scaling of box vectorstau_p = 0.2 ; time constant, in psref_p = 1.0 ; reference pressure, in barcompressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 Does anyone know how can I fix this? Which parameters should I change to reach the desired pressure and density?Thanks in advance.-Nima Azar -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GPU gromacs
Thanks Slizard. I need to get this simulation done in a week but does not have the right facilities. Is there anyone in the group with some high end GPU cards that can help me get this running. Cheers James On Tuesday, July 7, 2015, Szilárd Páll wrote: > Of course you can, but with such a low-end mobile GPU you may not even gain > performance from offloading computation from the CPU and additionally you > may have issues with cooling too. > > You can simply try comparing performance with "-nb cpu" and "-nb gpu" to > see if using the GPU improves performance at all. > > -- > Szilárd > > On Sat, Jul 4, 2015 at 1:40 PM, James Lord > wrote: > > > Hi All, > > I have a system with 300k atoms, I don't have access to HPC facilities, > Is > > it possible to run gromcas on GPU on a desktop with following graphic > card > > for up to 200-300 ns? > > > > 00:02.0 VGA compatible controller: Intel Corporation 3rd Gen Core > processor > > Graphics Controller (rev 09) > > 01:00.0 VGA compatible controller: NVIDIA Corporation GF108M [GeForce GT > > 635M] (rev a1) > > > > any thoughts is greatly appreciated. > > Cheers > > James > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org . > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org . -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_hbond
Hello Erik, I did the same. Thanks, Nilesh > Hi Nilesh, > > You could try gmx hbond -noda -r 0.25 -num hb.xvg, which should get the > contacts in the last column of hb.xvg. > > Kind regards, > Erik > >> On 10 Jul 2015, at 15:58, Nilesh Dhumal wrote: >> >> I don't understand why am I not getting hydrogen bond,if I use cufoff >> 0.25nm? >> >> Nilesh >> >>> But without contact you will need a full donor-hydrogen-acceptor triad >>> for >>> it to be registered, which is not what you want as far as I can tell. >>> >>> Erik >>> On 10 Jul 2015, at 15:17, Nilesh Dhumal wrote: This is index file [ O8-H18-1 ] 8 18 [ O8-H18-2 ] 4032 Found 1 donors and 2 acceptors Its look contact YES check the distance between accetpr---donor. I will run without contact. Nilesh > Hi Nilesh, > > Am not sure it accepts hydrogens as donors/acceptors even with > -contact. > How many donors and acceptors are found? > > Kind regards, > Erik > >> On 10 Jul 2015, at 14:37, Nilesh Dhumal >> wrote: >> >> I calculated number of hydrogen bond with cutoff 0.25 nm (Distance >> between >> hydrogen and O,acceptor) using g_hbond, >> >> g_hbond -f test.pdb -s 3.tpr -n hydrogen_1.ndx -num test_num.xvg >> -nonitacc >> -r 0.25 -contact -dist >> >> The found the calculated number of hydrogen bond along time are zero >> and >> -nan is the in hbdist.xvg file. >> I calculated the distance between hydrogen and oxygen using g_dist >> and >> the >> calculated the distance is less than 0.25 nm. >> >> Why am I getting zero number of hydrogen bonds using g_hbond (based >> on >> same cutoff )? >> >> Nilesh >> >> >> >>> Thanks. >>> >>> I will use two groups. >>> >>> Nilesh On 7/9/15 9:13 PM, Nilesh Dhumal wrote: >> >> >> On 7/9/15 9:02 PM, Nilesh Dhumal wrote: >>> Hello, >>> >>> I am calculating g_hbond for water system. I have a question >>> about >>> specifying two group for calculating hydrogen bond. >>> >>> Do I specify atoms in triplet(O-H---O)? >>> Can I specify O-H as one group (Donor-Hydrogen) and O in other >>> group >>> (Acceptor)? >> >> If the system is pure water, you do not need any special index >> groups. > > I have DMSO in the system. I just mentioned water to make it > simple. > I am interested in O--H---O(DMSO) interactions? > > How should I specify this? > > With one triplet O--H---O(DMSO) or two groups one O--H and second > O(DMSO) The latter - just use DMSO and water groups. O can be a donor or acceptor, and g_hbond intelligently figures out whether or not a given atom is a donor or acceptor (or both). -Justin >> >>> Default -r cutoff is 0.35nm. Is the distance between >>> hydrogen---acceptor >>> or distance between donor---acceptor? >> >> Read the first sentence of the help description. >> >> -Justin >> >> -- >> == >> >> Justin A. Lemkul, Ph.D. >> Ruth L. Kirschstein NRSA Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 629 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> http://mackerell.umaryland.edu/~jalemkul >> >> == >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List >> before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >> or >> send >> a mail to gmx-users-requ...@gromacs.org. >> > > -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>>
Re: [gmx-users] g_hbond
Hi Nilesh, You could try gmx hbond -noda -r 0.25 -num hb.xvg, which should get the contacts in the last column of hb.xvg. Kind regards, Erik > On 10 Jul 2015, at 15:58, Nilesh Dhumal wrote: > > I don't understand why am I not getting hydrogen bond,if I use cufoff 0.25nm? > > Nilesh > >> But without contact you will need a full donor-hydrogen-acceptor triad for >> it to be registered, which is not what you want as far as I can tell. >> >> Erik >> >>> On 10 Jul 2015, at 15:17, Nilesh Dhumal wrote: >>> >>> This is index file >>> >>> [ O8-H18-1 ] >>> 8 18 >>> [ O8-H18-2 ] >>> 4032 >>> >>> >>> Found 1 donors and 2 acceptors >>> >>> Its look contact YES check the distance between accetpr---donor. >>> >>> I will run without contact. >>> >>> Nilesh >>> Hi Nilesh, Am not sure it accepts hydrogens as donors/acceptors even with -contact. How many donors and acceptors are found? Kind regards, Erik > On 10 Jul 2015, at 14:37, Nilesh Dhumal > wrote: > > I calculated number of hydrogen bond with cutoff 0.25 nm (Distance > between > hydrogen and O,acceptor) using g_hbond, > > g_hbond -f test.pdb -s 3.tpr -n hydrogen_1.ndx -num test_num.xvg > -nonitacc > -r 0.25 -contact -dist > > The found the calculated number of hydrogen bond along time are zero > and > -nan is the in hbdist.xvg file. > I calculated the distance between hydrogen and oxygen using g_dist and > the > calculated the distance is less than 0.25 nm. > > Why am I getting zero number of hydrogen bonds using g_hbond (based on > same cutoff )? > > Nilesh > > > >> Thanks. >> >> I will use two groups. >> >> Nilesh >>> >>> On 7/9/15 9:13 PM, Nilesh Dhumal wrote: > > > On 7/9/15 9:02 PM, Nilesh Dhumal wrote: >> Hello, >> >> I am calculating g_hbond for water system. I have a question >> about >> specifying two group for calculating hydrogen bond. >> >> Do I specify atoms in triplet(O-H---O)? >> Can I specify O-H as one group (Donor-Hydrogen) and O in other >> group >> (Acceptor)? > > If the system is pure water, you do not need any special index > groups. I have DMSO in the system. I just mentioned water to make it simple. I am interested in O--H---O(DMSO) interactions? How should I specify this? With one triplet O--H---O(DMSO) or two groups one O--H and second O(DMSO) >>> >>> The latter - just use DMSO and water groups. O can be a donor or >>> acceptor, and >>> g_hbond intelligently figures out whether or not a given atom is a >>> donor >>> or >>> acceptor (or both). >>> >>> -Justin >>> > >> Default -r cutoff is 0.35nm. Is the distance between >> hydrogen---acceptor >> or distance between donor---acceptor? > > Read the first sentence of the help description. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > send > a mail to gmx-users-requ...@gromacs.org. > >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 629 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> == >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archiv
Re: [gmx-users] difference between steep and cg
Hi Ming Tang, See https://en.m.wikipedia.org/wiki/Gradient_descent It has a further link to CG. Cheers, Tsjerk On Jul 11, 2015 4:10 AM, "Ming Tang" wrote: > Dear Gromacs experts, > > I am quite confused about the difference between the energy minimization > algorithm steep and cg. According to my experience, MPI is not suitable for > cg. Sometimes, even if the system has already converged using steep > algorithm, it can be further minimized if one changes the algorithm to cg. > However, most of the publications choose to use steep descent algorithm. > Which one is more accurate? Is cg only suitable for specific analysis like > normal mode analysis? > > Thanks in advance, > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] question
Dear Mark, Thanks for your attention, If I want to use PRODRG server and not ATB for my ligand, how to modify charge and charge group number? I am beginner in this acse, please guide about that. Best wishes, Atila -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
