[gmx-users] -inter command
> Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > >1. Re: -inter command (Jo?o Henriques) >2. Rupture force definition (Rakesh Mishra) >3. Re: Can I get the fraction of solvent accessiblesurface area > using "gmx sasa"? (=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=) > > > -- > > Message: 1 > Date: Tue, 16 Jan 2018 08:30:10 +0100 > From: Jo?o Henriques > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] -inter command > Message-ID: > > Content-Type: text/plain; charset="UTF-8" Thank you so much Joao Sir for your kind response. 1. I have predicted the pka values for my protein using H++ server. 2. Based on the pka values, I have set the protonation states of the charged residues using -inter command for pH 9. 3.I have run my simulation at pH 9 (keeping charge of +8e) using gromacs 5.1.4 and gromos54a7 ff. After performing 100ns simulation, I didn't observed any change compared to control system. Can you provide any advice on it? Thank You Regards Zaved > A lot of OPs have the tendency to follow-up with private emails and I feel > it should stay public so other people might benefit from the information > as > well. Here is the rest of the conversation regarding this thread. > > """ > Dear Zaved, > > I'm not aware of any tutorials for Gromacs, and Gromacs does not support > constant-pH MD simulations straight out of the box. It must be (heavily) > modified. Amber comes pre-packaged with constant-pH functionality, I > believe. Still, you probably don't want to get involved in any of this. My > comment about it was merely to make you aware that changing the > protonation > states by hand doesn't make mean you're really simulating at a given pH. > Still, 99.9% of the people in this field do what you were wanting to do, > i.e., change the protonation states during pdb2gmx to whatever they feel > is > more representative of that residue at a given pH and then hit run. I also > do it, unless I'm studying something where charge regulation playes a > major > role, so by all means go ahead and try the simpler solution first. > > P.S.: Please avoid sending private messages about these subjects. It > started in gmx-users and should stay there for several reasons. The main > one is that other people might have the same problem and this information > might be useful for them as well. > > Best regards, > J > > On Tue, Jan 16, 2018 at 6:54 AM, wrote: > >> Dear Sir >> >> Thank you for your kind response regarding the -inter command. >> >> Sir can you guide / provide any tutorial for constant-pH MD simulation >> in >> gromacs (eg., to perform simulation at pH 9)? >> >> I shall be grateful to you for the same. >> >> Thank You >> >> Regards >> Zaved Hazarika >> Research Scholar >> Dept. Of Molecular Biology and Biotechnology, >> Tezpur University, >> Napam, 784028, >> Assam, >> India >> >> >> * * * D I S C L A I M E R * * * >> This e-mail may contain privileged information and is intended solely >> for >> the individual named. If you are not the named addressee you should not >> disseminate, distribute or copy this e-mail. Please notify the sender >> immediately by e-mail if you have received this e-mail in error and >> destroy >> it from your system. Though considerable effort has been made to deliver >> error free e-mail messages but it can not be guaranteed to be secure or >> error-free as information could be intercepted, corrupted, lost, >> destroyed, >> delayed, or may contain viruses. The recipient must verify the integrity >> of >> this e-mail message. > > """ > > J > > On Mon, Jan 15, 2018 at 11:51 AM, Jo?o Henriques < > joao.m.a.henriq...@gmail.com> wrote: > >> -inter sets the interactive mode for a bunch of other flags. Most are >> used >> for selecting the protonation states of the termini and other residues. >> It >> can also be used for interactive SS bridge selection. >> >> > "for setting the protonation state of charged amino acids in order to >> perform simulation at different pH?" >> >> Please note that changing the protonation states of the residues does >> not >> mean you're performing the simulation at a "different pH". A proper >> constant-pH MD simulation allows the residues to titrate in respect to >> the >> solution pH as well as the their "molecular environment". In this case, >> your residues will be "stuck" in a user defined protonation
[gmx-users] SDS initial setup
Dear Gromacs Users I am trying to simulate a protein with 200 SDS molecules. After inserting 200 molecules inside the box with the protein at the center (size of the cubic box is 324 nm3), few of the SDS molecules are outside the box from each side of the box. I have used the following command to insert the sds molecules: gmx insert-molecules -f prot.gro -ci sds.pdb -nmol 200 -o comp.gro Will it be appropriate to run simulation with this initial setup? Or do I need to make sure that entire sds molecules are inside the box. Kindly guide me. Thank You Regards Zaved H. * * * D I S C L A I M E R * * * This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail in error and destroy it from your system. Though considerable effort has been made to deliver error free e-mail messages but it can not be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, delayed, or may contain viruses. The recipient must verify the integrity of this e-mail message. -- 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] -inter command
On 1/18/18 7:02 AM, za...@tezu.ernet.in wrote: Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than "Re: Contents of gromacs.org_gmx-users digest..." Today's Topics: 1. Re: -inter command (Jo?o Henriques) 2. Rupture force definition (Rakesh Mishra) 3. Re: Can I get the fraction of solvent accessible surface area using "gmx sasa"? (=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=) -- Message: 1 Date: Tue, 16 Jan 2018 08:30:10 +0100 From: Jo?o Henriques To: gmx-us...@gromacs.org Subject: Re: [gmx-users] -inter command Message-ID: Content-Type: text/plain; charset="UTF-8" Thank you so much Joao Sir for your kind response. 1. I have predicted the pka values for my protein using H++ server. 2. Based on the pka values, I have set the protonation states of the charged residues using -inter command for pH 9. 3.I have run my simulation at pH 9 (keeping charge of +8e) using gromacs 5.1.4 and gromos54a7 ff. After performing 100ns simulation, I didn't observed any change compared to control system. Can you provide any advice on it? In what ways do the "pH 9" and "control" simulations differ? What do you define as "control" in this instance, default protonation by pdb2gmx? If that's the case, unless you have some very noncanonical pKa values, there's nothing that's really expected to be different between these two pH values, except perhaps the N-terminus itself. What are you trying to compare or calculate? Perhaps 100 ns is insufficient to observe whatever it is you're after. How have you quantified that there is no difference/change between these systems? -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] SDS initial setup
On 1/18/18 7:28 AM, za...@tezu.ernet.in wrote: Dear Gromacs Users I am trying to simulate a protein with 200 SDS molecules. After inserting 200 molecules inside the box with the protein at the center (size of the cubic box is 324 nm3), few of the SDS molecules are outside the box from each side of the box. I have used the following command to insert the sds molecules: gmx insert-molecules -f prot.gro -ci sds.pdb -nmol 200 -o comp.gro Will it be appropriate to run simulation with this initial setup? Or do I need to make sure that entire sds molecules are inside the box. There is no such thing as "outside" a periodic box. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] gmx enenrgy
On 1/18/18 12:38 AM, kordza...@aut.ac.ir wrote: Hi all when we use "gmx energy" what is the difference between LJ-(SR), LJ-14, Coulomb-14, Coulomb(SR)? those mentioned energies, give us energy interaction of total system. right? Not necessarily, because there may be long-range terms from PME or dispersion correction. if I want to determine interaction enenrgy for example, LJ, between two special species, not in total system, what should I do? Define energygrps in the .mdp file and re-evaluate the energies of the trajectory with mdrun -rerun. Note that for most force fields, this value has no physical significance. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] Umbrella Sampling
On 1/18/18 12:37 AM, Moradzadeh, Alireza wrote: Hi! I am trying to do umbrella sampling between two 2D-sheets. I did it according bevan lab tutorial the problem I encounter is that after pulling steps. I perform umbrella sampling with rate of 0.0 however, two sheets get back together and initial configuration and final configuration are totally different. Z_start = 0.91 nm and Z_Final = 0.51 nm. Any possible solution? Use a stronger force constant. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] tilt angle for POPC
On 1/18/18 12:24 AM, Mohsen Ramezanpour wrote: Dear Gromacs users, I am interested in calculation of tilt angle for the POPC headgroup (angle distribution between the P-N vector and Z axis). I am not sure if my approach is correct as my angle distribution does not seem reasonable. Given a bilayer with 200 lipids (100 lipids in each leaflet with resides 1-100 and 101-200 for upper and lower leaflets, respectively) simulated for 200 ns: gmx make_ndx -f SYSTEM.gro -o index.ndx keep 0 r 1-100 name 1 upperleaflet 1 & a P 1 & a N 2 | 3 name 4 vector q Next, I use: gmx gangle -f md.xtc -s md.tpr -n index.ndx -g1 vector -g2 z -b 10 -group1 -oh histogram.xvg -binw 0.01 and choose index group 4 and then Ctrl+D. Please let me know your opinion. I think I am doing something wrong, especially with the construction of P-N vector. What results do you get from this approach? What happens if you try to analyze only a single lipid? -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] six member ring won't stay flat
On 1/17/18 6:11 PM, Mark Abraham wrote: Hi, If you poke your finger into something, it isn't going to stay flat. :-) And to add on to this, in the CHARMM parametrization protocol, the first step is always an in vacuo geometry optimization (QM vs. MM comparison) to make sure the topology is sensible. If that doesn't check out, there are problems that can be easily spotted before subjecting the new residue to any other complicating factors like water and other parts of the protein. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] regarding pbc issue
On 1/17/18 12:06 PM, Rose wrote: Thank you so much,I've got it now. we know that for example 2 molecule can not stick to each other they just close enough till repulse each other. Now, imagine pulling, if I can not see "really broken" structures in classicalMD , so what would be my criterion and clue to say that:"that's enough, you shouldn't pull it MORE?" Totally, how can i know the Max pulling ? I have PMF schemes which show repulsion( after interaction distance the potential get less minus and tend to get more positive but they just stop in 0kJ and not any positive potential. It happened for every AA which i pull it through sheet, so i doubt to my results. A PMF of zero means the biased groups are (effectively) no longer interacting. You should expect this. This thread is well off topic of the original post; if you have further questions, start a new thread to avoid hijacking this one and complicating the archive further. -Justin Sorry for poor english With regards Sent from my iPhone On Jan 17, 2018, at 19:57, Justin Lemkul wrote: On 1/17/18 11:23 AM, Rose wrote: I mean, sometimes structures may really break or collapse, in these situations trjconv won't show these broken structures whole yes? just will show them broken (as they really are) yes? In the context of the question I was answering, "broken" means that it appears bonds have broken and molecules appear at either side of a periodic boundary. That instance is always fixed by proper use of trjconv. Bonds can't break or form during classical MD, so if trjconv leaves "broken" molecules behind, then you've got a topology issue. But I'd wager that about 99.999% of the cases that involve "broken" molecules are normal PBC issues and nothing more. But, to answer your question, no, trjconv won't fix a situation in which the user has supplied an incorrect topology. -Justin Sent from my iPhone On Jan 17, 2018, at 18:15, Justin Lemkul wrote: On 1/17/18 9:40 AM, Rose wrote: You mean if -pbc could make molecule whole,everything is ok, but if not it means the molecule was broken from first, yes? mdrun writes "broken" coordinates because the physics does not depend on our visualization convenience. Most programs account for PBC. Some don't. It is generally a safe practice to just make molecules whole as your first step in trjconv and avoid any ambiguity. -Justin Sent from my iPhone On Jan 17, 2018, at 16:19, Justin Lemkul wrote: On 1/17/18 5:51 AM, Vidya R wrote: Hi Justin, I got the same result as you said. What confused me was, when I viewed movie.pdb file generated by the following command, gmx trjconv -pbc nojump -s PRD-SMP3.gro -f PRD-SMP3.xtc -e 1.0 -n index.ndx -o movie.pdb two hydrogen molecules of my organic compound, were unbonded to my molecule (which is not supposed to be). They are far away from molecules (their bonds were broken) Is it a pbc problem? Because, when I used gmx trjconv -pbc whole -s PRD.tpr -f PRD.xtc -o trajwhole.xtc gmx trjconv -pbc nojump -s PRD.tpr -f trajwhole.xtc -o trajcluster.xtc gmx trjconv -pbc mol -center -s PRD.tpr -f trajcluster.xtc -o newtraj.xtc and created a .pdb file with newtraj.xtc, the whole molecule was intact. Making molecules whole should always be the first step. If you try to remove jumps with "broken" molecules, what you visualize will be garbage. A separate issue is with respect to the analysis programs - many are PBC-aware and can handle the original trajectory without manipulation. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] six member ring won't stay flat
I know what you mean, but I didn't see any other molecules getting too close to the ring :) On Wed, Jan 17, 2018 at 6:11 PM, Mark Abraham wrote: > Hi, > > If you poke your finger into something, it isn't going to stay flat. :-) > > Mark > > On Wed, Jan 17, 2018 at 9:44 PM MD wrote: > > > Hi Mark, > > Can you tell me more details about the ring's atoms interacting with an > > environment? What interactions did you mean? > > Thanks, > > Ming > > > > On Tue, Jan 16, 2018 at 6:43 AM, Mark Abraham > > wrote: > > > > > Hi, > > > > > > You still have many sources of problems (e.g. the warnings you > > suppressed, > > > the fact that your ring's atoms interact with an environment). What > > happens > > > when you minimize a capped peptide in vacuo? > > > > > > Mark > > > > > > On Tue, Jan 16, 2018 at 12:39 PM MD wrote: > > > > > > > Hi Justin, > > > > > > > > I got the itp and parameters of my side chain modified amino acid > from > > > > CHARMM-GUI and incorporated it into my protein structure, labeled > with > > > > HETATM. I made the atom types names consistent with charmm forcefield > > > which > > > > I used with gromacs and made sure overall the parameters look decent > > for > > > > now. After some fixing the grompp would run with no warnings, and I > > did a > > > > quick energy minimization, but ended up with a distorted six member > > > ring. I > > > > have the picture and my parameters attached. Your time is appreciated > > :) > > > > > > > > > > > > https://docs.google.com/document/d/1bjSq55HDLRsSVGqm5i0MRwI- > > > rgIesxy0QdIHm7tqTug/edit?usp=sharing > > > > > > > > Ming > > > > > > > > On Mon, Jan 15, 2018 at 7:53 PM, Justin Lemkul > > wrote: > > > > > > > > > > > > > > > > > > > On 1/15/18 7:45 PM, MD wrote: > > > > > > > > > >> Hi Gromacs, > > > > >> > > > > >> I have a modified side chain amino acid and it has a six member > ring > > > > >> attached to it. Regarding this ring I had dihedral angles taken > care > > > > with > > > > >> some 0s and some 180s. However, after minimization my structure > > looks > > > > very > > > > >> strange, the ring is not flat and the dihedral angles in my > settings > > > > >> didn't > > > > >> seem to apply to the minimized structure at all. Any thoughts? > > > > >> > > > > > > > > > > You're going to have to provide a lot more detail. You're > > parametrizing > > > > > something nonstandard, so there are plenty of places to make > > mistakes. > > > > > Without knowing your structure, the actual parameters and how > derived > > > and > > > > > validated them, there's nothing to do but guess. > > > > > > > > > > Keep in mind that rings are not necessarily perfectly planar, and > the > > > > > values set for dihedral phase offsets do not strictly mean the > values > > > > that > > > > > the dihedrals must adopt. > > > > > > > > > > -Justin > > > > > > > > > > -- > > > > > == > > > > > > > > > > Justin A. Lemkul, Ph.D. > > > > > Assistant Professor > > > > > Virginia Tech Department of Biochemistry > > > > > > > > > > 303 Engel Hall > > > > > 340 West Campus Dr. > > > > > Blacksburg, VA 24061 > > > > > > > > > > jalem...@vt.edu | (540) 231-3129 > > > > > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > > > > > > > > > == > > > > > > > > > > -- > > > > > 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. > > > > > -- > > 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://mail
Re: [gmx-users] six member ring won't stay flat
On Thu, Jan 18, 2018 at 7:43 AM, Justin Lemkul wrote: > > > On 1/17/18 6:11 PM, Mark Abraham wrote: > >> Hi, >> >> If you poke your finger into something, it isn't going to stay flat. :-) >> > > And to add on to this, in the CHARMM parametrization protocol, the first > step is always an in vacuo geometry optimization (QM vs. MM comparison) to > make sure the topology is sensible. If that doesn't check out, there are > problems that can be easily spotted before subjecting the new residue to > any other complicating factors like water and other parts of the protein. > > -Justin > Thank you Justin. What would you look at to make a judgement to see if the topology is sensible after the vacuo geometry optimization? Or as long as there were no errors or bad notes along the run it should be good? Thank you, Ming > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > -- > 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] six member ring won't stay flat
On 1/18/18 7:51 AM, MD wrote: On Thu, Jan 18, 2018 at 7:43 AM, Justin Lemkul wrote: On 1/17/18 6:11 PM, Mark Abraham wrote: Hi, If you poke your finger into something, it isn't going to stay flat. :-) And to add on to this, in the CHARMM parametrization protocol, the first step is always an in vacuo geometry optimization (QM vs. MM comparison) to make sure the topology is sensible. If that doesn't check out, there are problems that can be easily spotted before subjecting the new residue to any other complicating factors like water and other parts of the protein. -Justin Thank you Justin. What would you look at to make a judgement to see if the topology is sensible after the vacuo geometry optimization? Or as long as there were no errors or bad notes along the run it should be good? You look at the structure to see if it is sensible (and here, sensible is defined as properly reproducing QM-optimized geometries and/or known high-resolution experimental geometries - start with QM and compare against empirical evidence later). The absence of errors or notes when executing grompp tells you precisely nothing about the integrity of the physical model; it only tells you if you've forgotten to do something. I can populate every parameter field with absolute garbage and grompp will happily carry on preparing my doomed simulation :) -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] Three different diffusivities by "gmx msd" /
Dear GROMACS community, evaluating the diffusivity of as single dodecyl sulfate (DS) anion, I use a small trajectory chunk "md_1.trr" 5 ps (500 frames) long for testing purposes. The .trr has been stripped of any atoms except the 42 ones forming the DS chain (12H25SO4). What is more, I prepared an index file DS_selection.ndx with the content [ Surfactant ] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 in order to select the molecule of interest explicitly. As far as I understand the GMX 2016.4 manual and help, the commad gmx msd -f md_1.trr -s md.tpr -o atom_wise_msd.xvg -n DS_selection.ndx should yield the atom-wise evaluated MSD averaged over all 42 atoms for each timestep. "atom_wise_msd.xvg" contains the comment # MSD gathered over 4.99 ps with 1 restarts # Diffusion constants fitted from time 0.5 to 4.49 ps # D[Surfactant] = 1.8305 (+/- 1.3704) (1e-5 cm^2/s) which I understand as the atom-averaged diffusivity. On the other hand, gmx msd -f md_1.trr -s md.tpr -o mol_wise_msd.xvg -mol mol_wise_D.xvg -n DS_selection.ndx should yield MSD (and diffusivity D) for the molecule's COM, and consequently a different value D # MSD gathered over 4.99 ps with 1 restarts # Diffusion constants fitted from time 0.5 to 4.49 ps # D[Surfactant] = 1.5575 (+/- 1.3521) (1e-5 cm^2/s) is found within "mol_wise_msd.xvg". So far, so good, my understanding is correct up until here? Now, looking at the latter command's stdout, I have = 1.1395 Std. Dev. = -nan Error = -nan Fitting from 0.5 to 4.49 ps D[Surfactant] 1.5575 (+/- 1.3521) 1e-5 cm^2/s and in the file "mol_wise_D.xvg" of course just one entry for the single DS molecule @ title "Diffusion Coefficients / Molecule" @ xaxis label "Molecule" @ yaxis label "D" @TYPE xy 0 1.13953 Here, I am confused. How does the third value for D arise? Naturally, I would have expected "mol_wise_D.xvg" to list the same value of D = 1.5575 as found within the comment of "mol_wise_msd.xvg". I am looking forward to a clarifying answer, as I could not find any notes on this discrepancy in the documentation. Is it maybe possible that the = 1.1395 is evaluated over all 5ps, whereas D[Surfactant] = 1.5575is fitted only on the 80% trajectory from 0.5 to 4.49 ps? If so, some clear hint towards this fact would be appreciated in the "gmx help msd" text. A different topic: I could not find any option for "gmx msd" to evaluate a trajectory frame-wise without loading the whole file into memory. When applied onto a several GB .trr, even with relatively small "-trestart”, GMX would continuously eat up memory until the job would be canceled due to running out of the node's 128 GB RAM. Maybe any undocumented option hidden somewhere? Here the output of "gmx --version" GROMACS: gmx, version 2016.4 Executable: /work/ws/nemo/fr_lp1029-IMTEK_SIMULATION-0/gromacs_2016.4_gnu/bin/gmx Data prefix: /work/ws/nemo/fr_lp1029-IMTEK_SIMULATION-0/gromacs_2016.4_gnu Working dir: /work/ws/nemo/fr_jh1130-201708-0/jobs/gmxlab/sds/201801/farafonov2017developing/1ds/rtp/GAFF-SPC Command line: gmx --version GROMACS version: 2016.4 Precision: single Memory model: 64 bit MPI library: thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32) GPU support: disabled SIMD instructions: AVX2_256 FFT library: fftw-3.3.7-sse2-avx-avx2-avx2_128 RDTSCP usage: enabled TNG support: enabled Hwloc support: hwloc-1.11.0 Tracing support: disabled Built on: Wed Dec 13 10:46:41 CET 2017 Built by: fr_jh1...@int02.nemo.privat [CMAKE] Build OS/arch: Linux 3.10.0-693.5.2.el7.x86_64 x86_64 Build CPU vendor: Intel Build CPU brand: Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz Build CPU family: 6 Model: 79 Stepping: 1 Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /opt/bwhpc/common/compiler/gnu/5.2.0/bin/gcc GNU 5.2.0 C compiler flags: -march=core-avx2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast C++ compiler: /opt/bwhpc/common/compiler/gnu/5.2.0/bin/g++ GNU 5.2.0 C++ compiler flags: -march=core-avx2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast Thanks for your help. Best regards, -- Johannes Hörmann University of Freiburg IMTEK - Department of Microsystems Engineering Laboratory for Simulation Georges-Köhler-Allee 103, Room 03 020 79110 Freibur
Re: [gmx-users] six member ring won't stay flat
Coolbeans! Thank you Justin :) Ming On Jan 18, 2018 7:54 AM, "Justin Lemkul" wrote: > > > On 1/18/18 7:51 AM, MD wrote: > >> On Thu, Jan 18, 2018 at 7:43 AM, Justin Lemkul wrote: >> >> >>> On 1/17/18 6:11 PM, Mark Abraham wrote: >>> >>> Hi, If you poke your finger into something, it isn't going to stay flat. :-) And to add on to this, in the CHARMM parametrization protocol, the first >>> step is always an in vacuo geometry optimization (QM vs. MM comparison) >>> to >>> make sure the topology is sensible. If that doesn't check out, there are >>> problems that can be easily spotted before subjecting the new residue to >>> any other complicating factors like water and other parts of the protein. >>> >>> -Justin >>> >>> Thank you Justin. What would you look at to make a judgement to see if >> the topology is sensible after the vacuo geometry optimization? Or as long >> as there were no errors or bad notes along the run it should be good? >> > > You look at the structure to see if it is sensible (and here, sensible is > defined as properly reproducing QM-optimized geometries and/or known > high-resolution experimental geometries - start with QM and compare against > empirical evidence later). > > The absence of errors or notes when executing grompp tells you precisely > nothing about the integrity of the physical model; it only tells you if > you've forgotten to do something. I can populate every parameter field with > absolute garbage and grompp will happily carry on preparing my doomed > simulation :) > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > -- > 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] six member ring won't stay flat
I have a question related to charmm. Does charmm have a name/structure chart for all the parametrized molecules? I want to borrow some parameters info from those molecules but often I can't quickly figure out what they are. Ming On Jan 18, 2018 8:18 AM, "MD" wrote: > Coolbeans! Thank you Justin :) > Ming > > On Jan 18, 2018 7:54 AM, "Justin Lemkul" wrote: > >> >> >> On 1/18/18 7:51 AM, MD wrote: >> >>> On Thu, Jan 18, 2018 at 7:43 AM, Justin Lemkul wrote: >>> >>> On 1/17/18 6:11 PM, Mark Abraham wrote: Hi, > > If you poke your finger into something, it isn't going to stay flat. > :-) > > And to add on to this, in the CHARMM parametrization protocol, the first step is always an in vacuo geometry optimization (QM vs. MM comparison) to make sure the topology is sensible. If that doesn't check out, there are problems that can be easily spotted before subjecting the new residue to any other complicating factors like water and other parts of the protein. -Justin Thank you Justin. What would you look at to make a judgement to see if >>> the topology is sensible after the vacuo geometry optimization? Or as >>> long >>> as there were no errors or bad notes along the run it should be good? >>> >> >> You look at the structure to see if it is sensible (and here, sensible is >> defined as properly reproducing QM-optimized geometries and/or known >> high-resolution experimental geometries - start with QM and compare against >> empirical evidence later). >> >> The absence of errors or notes when executing grompp tells you precisely >> nothing about the integrity of the physical model; it only tells you if >> you've forgotten to do something. I can populate every parameter field with >> absolute garbage and grompp will happily carry on preparing my doomed >> simulation :) >> >> -Justin >> >> -- >> == >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Virginia Tech Department of Biochemistry >> >> 303 Engel Hall >> 340 West Campus Dr. >> Blacksburg, VA 24061 >> >> jalem...@vt.edu | (540) 231-3129 >> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html >> >> == >> >> -- >> 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] six member ring won't stay flat
On 1/18/18 8:46 AM, MD wrote: I have a question related to charmm. Does charmm have a name/structure chart for all the parametrized molecules? I want to borrow some parameters info from those molecules but often I can't quickly figure out what they are. Not in one places, but every CHARMM RTF and stream file contains an ASCII drawing and full name of every species in the residue entries. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] SDS initial setup
Besides the fact that there cannot be molecules outside a periodic box, are you sure that you want such a high SDS concentration? You are nearly 15 times over the cmc, in the real world you would most likely end up with a hydrated SDS crystals (Mol. Cryst. Liq. Cryst., Vol. 549:pp. 160–165, 2011) On Thu, Jan 18, 2018 at 10:39 AM, Justin Lemkul wrote: > > > On 1/18/18 7:28 AM, za...@tezu.ernet.in wrote: > >> Dear Gromacs Users >> >> I am trying to simulate a protein with 200 SDS molecules. >> >> After inserting 200 molecules inside the box with the protein at the >> center (size of the cubic box is 324 nm3), few of the SDS molecules are >> outside the box from each side of the box. >> >> I have used the following command to insert the sds molecules: >> >> gmx insert-molecules -f prot.gro -ci sds.pdb -nmol 200 -o comp.gro >> >> Will it be appropriate to run simulation with this initial setup? Or do I >> need to make sure that entire sds molecules are inside the box. >> > > There is no such thing as "outside" a periodic box. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > > -- > 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. > -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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] six member ring won't stay flat
On Thu, Jan 18, 2018 at 8:48 AM, Justin Lemkul wrote: > > > On 1/18/18 8:46 AM, MD wrote: > >> I have a question related to charmm. Does charmm have a name/structure >> chart for all the parametrized molecules? I want to borrow some parameters >> info from those molecules but often I can't quickly figure out what they >> are. >> > > Not in one places, but every CHARMM RTF and stream file contains an ASCII > drawing and full name of every species in the residue entries. > > > -Justin > Justin, the CHARMM forcefield I downloaded has a folder of files including merged.rtp, ffbonded.itp... but I didn't see any rtf file or any file that has ASCII drawings. I am sure I am missing something obvious here. Do you mind giving me a quick link/example please? Thanks, Ming > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > -- > 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] six member ring won't stay flat
On 1/18/18 9:04 AM, MD wrote: On Thu, Jan 18, 2018 at 8:48 AM, Justin Lemkul wrote: On 1/18/18 8:46 AM, MD wrote: I have a question related to charmm. Does charmm have a name/structure chart for all the parametrized molecules? I want to borrow some parameters info from those molecules but often I can't quickly figure out what they are. Not in one places, but every CHARMM RTF and stream file contains an ASCII drawing and full name of every species in the residue entries. -Justin Justin, the CHARMM forcefield I downloaded has a folder of files including merged.rtp, ffbonded.itp... but I didn't see any rtf file or any file that has ASCII drawings. I am sure I am missing something obvious here. Do you mind giving me a quick link/example please? You need to be looking at the CHARMM files, not GROMACS files. http://mackerell.umaryland.edu/charmm_ff.shtml#charmm -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] six member ring won't stay flat
whoops, Thank you :)) On Thu, Jan 18, 2018 at 9:05 AM, Justin Lemkul wrote: > > > On 1/18/18 9:04 AM, MD wrote: > >> On Thu, Jan 18, 2018 at 8:48 AM, Justin Lemkul wrote: >> >> >>> On 1/18/18 8:46 AM, MD wrote: >>> >>> I have a question related to charmm. Does charmm have a name/structure chart for all the parametrized molecules? I want to borrow some parameters info from those molecules but often I can't quickly figure out what they are. Not in one places, but every CHARMM RTF and stream file contains an >>> ASCII >>> drawing and full name of every species in the residue entries. >>> >>> >>> -Justin >>> >>> Justin, the CHARMM forcefield I downloaded has a folder of files >> including >> merged.rtp, ffbonded.itp... but I didn't see any rtf file or any file that >> has ASCII drawings. I am sure I am missing something obvious here. Do you >> mind giving me a quick link/example please? >> > > You need to be looking at the CHARMM files, not GROMACS files. > > http://mackerell.umaryland.edu/charmm_ff.shtml#charmm > > -Justin > > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > -- > 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] gmx enenrgy
Hello Dr.Lemkul Thank you very much for your answer I try to do it. Regards Azadeh -- This email was Anti Virus checked by Security Gateway. -- 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] Recentering a protein
Hi I am new to gromacs (using v. 2016.4) and need to check the following steps for my system. 01. I have prepared the system with Amber 14, minimized, heated to 300K, equilibrated 02. Then I used Acpype to convert the amber top and equilibrated rst file to gromacs .top and .gro files03. Changing Na+ to NA and WAT to SOL and H and O of water to HW1 HW2 and OW04. Doing a CG minimization again with gromacs.05. Doing a NPT with gromacs06. Running MD simulation with gromacs. Is this procedure correct or do I need any modification? In Amber we used to run MD for 5 ns, then recenter then relaunch from the last rst file. The same case will be with gromacs.Is there a script I can find to recenter and relunch the process automatically? Another thing after doing the minimization, I cannot recenter the protein by trjconv command gmx trjconv -f em.gro -s em.tpr -o em_1.gro -center -pbc mol -ur compact>> selecting 1 to center protein>> selecting 0 to get the whole system output https://drive.google.com/open?id=13lGcj52NpteRPTBHFJOKlXZ9dUliezqd In this link you have The acp.gro and acp.top file produced from Acpype with modifications to Na and watermdp files for Min, NPT, MD, please check themAnd the em.gro the file produced after minimization which cannot be centered Many thanks Kind Regards,Ahmed -- 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] tilt angle for POPC
Hi Justin, On Thu, Jan 18, 2018 at 5:42 AM, Justin Lemkul wrote: > > > On 1/18/18 12:24 AM, Mohsen Ramezanpour wrote: > >> Dear Gromacs users, >> >> I am interested in calculation of tilt angle for the POPC headgroup (angle >> distribution between the P-N vector and Z axis). >> I am not sure if my approach is correct as my angle distribution does not >> seem reasonable. >> >> Given a bilayer with 200 lipids (100 lipids in each leaflet with >> resides 1-100 and 101-200 for upper and lower leaflets, respectively) >> simulated for 200 ns: >> >> gmx make_ndx -f SYSTEM.gro -o index.ndx >> keep 0 >> r 1-100 >> name 1 upperleaflet >> 1 & a P >> 1 & a N >> 2 | 3 >> name 4 vector >> q >> >> Next, I use: >> gmx gangle -f md.xtc -s md.tpr -n index.ndx -g1 vector -g2 z >> -b >> 10 -group1 -oh histogram.xvg -binw 0.01 >> >> and choose index group 4 and then Ctrl+D. >> >> Please let me know your opinion. I think I am doing something wrong, >> especially with the construction of P-N vector. >> > > What results do you get from this approach? > A normal distribution centered around 105 with a high pick standing out around 90. I expected it to be around ~73-77 > > What happens if you try to analyze only a single lipid? > I get an approximate normal distribution centered around 100 degrees. I have two systems, one is salt free and the other one has 0.15 M NaCL salt. The shape of histograms is the same. I had to separate the leaflets, right? So, any idea why this is happening? > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > -- > 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. > -- *Rewards work better than punishment ...* -- 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] tilt angle for POPC
And, I used Charmm36 FF for simulations in Gromacs v. 2016.3 Cheers, Mohsen On Thu, Jan 18, 2018 at 11:28 AM, Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Hi Justin, > > On Thu, Jan 18, 2018 at 5:42 AM, Justin Lemkul wrote: > >> >> >> On 1/18/18 12:24 AM, Mohsen Ramezanpour wrote: >> >>> Dear Gromacs users, >>> >>> I am interested in calculation of tilt angle for the POPC headgroup >>> (angle >>> distribution between the P-N vector and Z axis). >>> I am not sure if my approach is correct as my angle distribution does not >>> seem reasonable. >>> >>> Given a bilayer with 200 lipids (100 lipids in each leaflet with >>> resides 1-100 and 101-200 for upper and lower leaflets, respectively) >>> simulated for 200 ns: >>> >>> gmx make_ndx -f SYSTEM.gro -o index.ndx >>> keep 0 >>> r 1-100 >>> name 1 upperleaflet >>> 1 & a P >>> 1 & a N >>> 2 | 3 >>> name 4 vector >>> q >>> >>> Next, I use: >>> gmx gangle -f md.xtc -s md.tpr -n index.ndx -g1 vector -g2 z >>> -b >>> 10 -group1 -oh histogram.xvg -binw 0.01 >>> >>> and choose index group 4 and then Ctrl+D. >>> >>> Please let me know your opinion. I think I am doing something wrong, >>> especially with the construction of P-N vector. >>> >> >> What results do you get from this approach? >> > A normal distribution centered around 105 with a high pick standing out > around 90. > I expected it to be around ~73-77 > > >> >> What happens if you try to analyze only a single lipid? >> > I get an approximate normal distribution centered around 100 degrees. > > > I have two systems, one is salt free and the other one has 0.15 M NaCL > salt. > The shape of histograms is the same. > > I had to separate the leaflets, right? > So, any idea why this is happening? > >> >> -Justin >> >> -- >> == >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Virginia Tech Department of Biochemistry >> >> 303 Engel Hall >> 340 West Campus Dr. >> Blacksburg, VA 24061 >> >> jalem...@vt.edu | (540) 231-3129 >> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html >> >> == >> >> -- >> 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. >> > > > > -- > *Rewards work better than punishment ...* > -- *Rewards work better than punishment ...* -- 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] tilt angle for POPC
Looking at index file made in the above mentioned way, as way as the following way: gmx make_ndx -f SYSTEM.gro -o index.ndx keep 0 r 1-100 name 1 upperleaflet 1 & a P N name 2 vector q gave the same results. Interestingly, even if I make the index file like: gmx make_ndx -f SYSTEM.gro -o index.ndx keep 0 r 1-100 name 1 upperleaflet 1 & a N P name 2 vector q The index file (i.e. the order and numbers in the index file) for group 2 is exactly the same, i.e. will give the N->P vector, not P->N. So, I think this is why there was a shift to more than 90 degrees. doing (180-alpha) gave the P->N angle distribution. STILL, I do not know why there is a pick standing out around 90 degrees. It is very sharp narrow pick. Other tilt angle distributions I have seem do not show such a pick. Thanks in advance for your comments and help On Thu, Jan 18, 2018 at 11:29 AM, Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > And, I used Charmm36 FF for simulations in Gromacs v. 2016.3 > > Cheers, > Mohsen > > On Thu, Jan 18, 2018 at 11:28 AM, Mohsen Ramezanpour < > ramezanpour.moh...@gmail.com> wrote: > >> Hi Justin, >> >> On Thu, Jan 18, 2018 at 5:42 AM, Justin Lemkul wrote: >> >>> >>> >>> On 1/18/18 12:24 AM, Mohsen Ramezanpour wrote: >>> Dear Gromacs users, I am interested in calculation of tilt angle for the POPC headgroup (angle distribution between the P-N vector and Z axis). I am not sure if my approach is correct as my angle distribution does not seem reasonable. Given a bilayer with 200 lipids (100 lipids in each leaflet with resides 1-100 and 101-200 for upper and lower leaflets, respectively) simulated for 200 ns: gmx make_ndx -f SYSTEM.gro -o index.ndx keep 0 r 1-100 name 1 upperleaflet 1 & a P 1 & a N 2 | 3 name 4 vector q Next, I use: gmx gangle -f md.xtc -s md.tpr -n index.ndx -g1 vector -g2 z -b 10 -group1 -oh histogram.xvg -binw 0.01 and choose index group 4 and then Ctrl+D. Please let me know your opinion. I think I am doing something wrong, especially with the construction of P-N vector. >>> >>> What results do you get from this approach? >>> >> A normal distribution centered around 105 with a high pick standing out >> around 90. >> I expected it to be around ~73-77 >> >> >>> >>> What happens if you try to analyze only a single lipid? >>> >> I get an approximate normal distribution centered around 100 degrees. >> >> >> I have two systems, one is salt free and the other one has 0.15 M NaCL >> salt. >> The shape of histograms is the same. >> >> I had to separate the leaflets, right? >> So, any idea why this is happening? >> >>> >>> -Justin >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Assistant Professor >>> Virginia Tech Department of Biochemistry >>> >>> 303 Engel Hall >>> 340 West Campus Dr. >>> Blacksburg, VA 24061 >>> >>> jalem...@vt.edu | (540) 231-3129 >>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html >>> >>> == >>> >>> -- >>> 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. >>> >> >> >> >> -- >> *Rewards work better than punishment ...* >> > > > > -- > *Rewards work better than punishment ...* > -- *Rewards work better than punishment ...* -- 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] tilt angle for POPC
I did more tests and here are the conclusions for the pick mentioned earlier. The pick appears when the -binw gets smaller and smaller. For the default value of gangle (which is 1), one cannot detect such a pick and you will get a normal distribution. Even for a -binw of 0.1 everything looks fine. However, for -binw of lower than 0.1, e.g. 0.5 or so, the picks appear. Well, is this a problem with POPC simulation, POPC topology, POPC parameters, the algorithm behind gangle, or it is what is really happening and we do not detect it due to the NOT enough Small value of -binw in the histogram? I vote for the last option. Cheers, On Thu, Jan 18, 2018 at 12:07 PM, Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Looking at index file made in the above mentioned way, as way as the > following way: > > gmx make_ndx -f SYSTEM.gro -o index.ndx > keep 0 > r 1-100 > name 1 upperleaflet > 1 & a P N > name 2 vector > q > > gave the same results. > Interestingly, even if I make the index file like: > gmx make_ndx -f SYSTEM.gro -o index.ndx > keep 0 > r 1-100 > name 1 upperleaflet > 1 & a N P > name 2 vector > q > > > The index file (i.e. the order and numbers in the index file) for group 2 > is exactly the same, i.e. will give the N->P vector, not P->N. > So, I think this is why there was a shift to more than 90 degrees. > doing (180-alpha) gave the P->N angle distribution. > > STILL, I do not know why there is a pick standing out around 90 degrees. > It is very sharp narrow pick. > Other tilt angle distributions I have seem do not show such a pick. > > Thanks in advance for your comments and help > > > On Thu, Jan 18, 2018 at 11:29 AM, Mohsen Ramezanpour < > ramezanpour.moh...@gmail.com> wrote: > >> And, I used Charmm36 FF for simulations in Gromacs v. 2016.3 >> >> Cheers, >> Mohsen >> >> On Thu, Jan 18, 2018 at 11:28 AM, Mohsen Ramezanpour < >> ramezanpour.moh...@gmail.com> wrote: >> >>> Hi Justin, >>> >>> On Thu, Jan 18, 2018 at 5:42 AM, Justin Lemkul wrote: >>> On 1/18/18 12:24 AM, Mohsen Ramezanpour wrote: > Dear Gromacs users, > > I am interested in calculation of tilt angle for the POPC headgroup > (angle > distribution between the P-N vector and Z axis). > I am not sure if my approach is correct as my angle distribution does > not > seem reasonable. > > Given a bilayer with 200 lipids (100 lipids in each leaflet with > resides 1-100 and 101-200 for upper and lower leaflets, respectively) > simulated for 200 ns: > > gmx make_ndx -f SYSTEM.gro -o index.ndx > keep 0 > r 1-100 > name 1 upperleaflet > 1 & a P > 1 & a N > 2 | 3 > name 4 vector > q > > Next, I use: > gmx gangle -f md.xtc -s md.tpr -n index.ndx -g1 vector -g2 > z -b > 10 -group1 -oh histogram.xvg -binw 0.01 > > and choose index group 4 and then Ctrl+D. > > Please let me know your opinion. I think I am doing something wrong, > especially with the construction of P-N vector. > What results do you get from this approach? >>> A normal distribution centered around 105 with a high pick standing out >>> around 90. >>> I expected it to be around ~73-77 >>> >>> What happens if you try to analyze only a single lipid? >>> I get an approximate normal distribution centered around 100 degrees. >>> >>> >>> I have two systems, one is salt free and the other one has 0.15 M NaCL >>> salt. >>> The shape of histograms is the same. >>> >>> I had to separate the leaflets, right? >>> So, any idea why this is happening? >>> -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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. >>> >>> >>> >>> -- >>> *Rewards work better than punishment ...* >>> >> >> >> >> -- >> *Rewards work better than punishment ...* >> > > > > -- > *Rewards work better than punishment ...* > -- *Rewards work better than punishment ...* -- 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
[gmx-users] An conda package for installing gromacs 4.5.5 on 64-bit linux system
Hi gromacs users: I just wrote this to share that I write a conda package let you to install gromacs 4.5.5 on 64-bit linux system: https://anaconda.org/hsiaoyi0504/gromacs The objective of this package is to let people build applications based on gromacs more easier, such as prediction system based on result produced by gromacs. Some similar work for gromas 4.6.5 is in bioconda: https://anaconda.org/bioconda/gromacs. If you have any question or suggestion, you can email me or leave message on issue system of repo for the source code to build the conda package. https://github.com/hsiaoyi0504/conda_gromacs_4.5.5. Best regards, Leo (Yi Hsiao) -- 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] An conda package for installing gromacs 4.5.5 on 64-bit linux system
Why 4.5.5? On Thu, Jan 18, 2018 at 11:26 PM, 蕭毅 wrote: > Hi gromacs users: > > I just wrote this to share that I write a conda package let you to install > gromacs 4.5.5 on 64-bit linux system: > https://anaconda.org/hsiaoyi0504/gromacs > > The objective of this package is to let people build applications based on > gromacs more easier, such as prediction system based on result produced by > gromacs. Some similar work for gromas 4.6.5 is in bioconda: > https://anaconda.org/bioconda/gromacs. If you have any question or > suggestion, you can email me or leave message on issue system of repo for > the source code to build the conda package. > https://github.com/hsiaoyi0504/conda_gromacs_4.5.5. > > Best regards, > Leo (Yi Hsiao) > -- > 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] Rupture force definition
Dear Justin Thanks for your explanation . Yes I am agree that it will depend on the k value and path direction. Let suppose we map the experimental spring constant and rate then it will be some how relevant for my study. My another query is the same from umbrella sampling of puling code. If I restrain some different molecule (let C ) and give the reference molecule (let B) and pulling molecule (Let A), then I found that , when I pull molecule A in + x direction then C has immobility while molecule B is feeling opposite force w. r. t. molecule A. i. e. if molecule A is moving along + x direction then reference molecule B starts to move in - x direction. Now I want to know that in pulling code, does reference molecule and pulling molecule connected with imaginary spring, due to this newton third law is applying here. Best On Wed, Jan 17, 2018 at 6:20 PM, Justin Lemkul wrote: > > > On 1/17/18 7:09 AM, Rakesh Mishra wrote: > >> Dear, >> Justin >> >> >> >> I have one query regarding pulling of si-rNA (having chain-a and >> chain-b). >> Here, I am pulling 3' end of chain-a and fixed 3' end of chain-b >> (diagonally apposite ). I am doing pulling using gromacs with constant >> velocity rate using Umbrella sampling. after finalization of pulling >> before >> umbrella sampling, we got two output file i.e. >> >> 1- force/time (f= force) >> 2- x/time (x= pulling distance between two ends) >> >> in first case of f/t, initially force increases and then after some time, >> force starts >> to decrease (looks like gaussian curve, not exactly gaussian, because lot >> of fluctuation). So my question is that, what this peak (of increasing and >> decreasing curve ) represents. can I define this peak as a rupture force >> or >> breaking force of two strands of si-rna or something else. >> >> > If you change the force constant, you'll get a different maximum force, so > I wouldn't ascribe any real physical property to this number. The maximum > force can inform you about the interactions that are perhaps most relevant > to stability, but that's also a path-dependent behavior; if you pull in a > different direction, you will probably get a different result. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > -- > 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. -- * Rakesh Kumar Mishra* * (RA)CSD SINP Kolkata, India* *E-mail - rakesh.mis...@saha.ac.in * *Phone n. +91 9473662491, +91877749632* -- 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.