[gmx-users] pH dependent simulation
Hello Everyone I am trying to simulate a protein at two pH (7.4 and 9.0) using gromacs 5.1.4. The protein has no missing residues. Optimal pH range is 6.0 to 9.0 and pI of the protein is 11.4. It has 9 negatively and 17 positively charged residues. However upon predicting the pKa values using H++ server, I am getting the same pKa values for all the charged residues (at pH 7.4 and pH 9). And the total charge of +8e is also same at both pH 7.4 and 9.0. (Instead it should have different pKa values at pH 7 and 9). Whether I am in the right direction or doing something wrong!!! Can anyone kindly suggest me how to proceed further? Any suggestion is appreciated. Thank You Zaved * * * 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] gromacs.org_gmx-users Digest, Vol 163, Issue 116
> 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. Pdb2gmx melts molecules due to bad distances (GIANMARCO BARTALINI) >2. Not enough memory. Failed to realloc (RAHUL SURESH) >3. Re: pH dependent simulation (Justin Lemkul) >4. Re: pH dependent simulation (Justin Lemkul) >5. Re: Pdb files generated on Lincs warning (Justin Lemkul) >6. Re: Fatal error in grompp (Justin Lemkul) > > > -- > > Message: 1 > Date: Mon, 27 Nov 2017 12:04:04 +0100 > From: GIANMARCO BARTALINI > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] Pdb2gmx melts molecules due to bad distances > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > > Hello guys, I produced a system "protein + lipid membrane" using the > online > tool CHARMM-GUI. Since I need to use the Amber force field, I added the > Lipids17 force field inside Gromacs. The implementation should work fine, > since the conversion of an equilibrated structure produces a nice and > correct gro file. But when I try to convert the (not minimized) PDB file > that I get from CHARMM-GUI using pdb2gmx, I get a gro structure where many > lipid molecules are melted together (due to their bad distances). If I use > this structure for a minimization, the calculation stops due to bad > energies. Do you know how to solve this issue? > Thank you in advance, > > Gianmarco > > > -- > > Message: 2 > Date: Mon, 27 Nov 2017 17:47:36 +0530 > From: RAHUL SURESH > To: gmx-us...@gromacs.org > Subject: [gmx-users] Not enough memory. Failed to realloc > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > > Dear Users > > I am trying to carryout protein-metal interaction using charmm36 ff. > During > solvation *"gmx solvate -cp cuNew.gro -cs spc216.gro -p cu.top -o > solv.gro" > *i receive a error stating > > > > > > > > > *"Fatal error:Not enough memory. Failed to realloc 3094482528 bytes for > atoms_->atom,atoms_->atom=0(called from > file/home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/topology/atomsbuilder.cpp,line > 86)". * > I have enough space to carry out this simulation and I am using 2016 > version of gromacs. > > I couldnt diagonise the error exactly. Any help on this will be of great > use. > > Thank you > > -- > *Regards,* > *Rahul Suresh* > *Research Scholar* > *Bharathiar University* > *Coimbatore* > > > -- > > Message: 3 > Date: Mon, 27 Nov 2017 08:31:18 -0500 > From: Justin Lemkul > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] pH dependent simulation > Message-ID: > Content-Type: text/plain; charset=utf-8; format=flowed > > > Thank you sir for the explanation. > On 11/26/17 11:09 PM, za...@tezu.ernet.in wrote: >> Hello Everyone >> >> I am trying to simulate a protein at two pH (7.4 and 9.0) using >> gromacs 5.1.4. The protein has no missing residues. Optimal pH range is >> 6.0 to 9.0 and pI of the protein is 11.4. It has 9 negatively and 17 >> positively charged residues. >> >> However upon predicting the pKa values using H++ server, I am getting >> the >> same pKa values for all the charged residues (at pH 7.4 and pH 9). And >> the >> total charge of +8e is also same at both pH 7.4 and 9.0. (Instead it >> should have different pKa values at pH 7 and 9). > > Why do you expect that? There are no amino acids with pKa in that range, > so nothing should change unless there are unique microenvironments that > shift canonical pKa values. As H++ has not detected any, likely your > protein behaves canonically. You can confirm your calculated pKa values > with another method, like PROPKA, to be sure. > > -Justin > >> Whether I am in the right direction or doing something wrong!!! >> >> Can anyone kindly suggest me how to proceed further? >> >> Any suggestion is appreciated. >
Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 163, Issue 116
> 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. Pdb2gmx melts molecules due to bad distances (GIANMARCO BARTALINI) >2. Not enough memory. Failed to realloc (RAHUL SURESH) >3. Re: pH dependent simulation (Justin Lemkul) >4. Re: pH dependent simulation (Justin Lemkul) >5. Re: Pdb files generated on Lincs warning (Justin Lemkul) >6. Re: Fatal error in grompp (Justin Lemkul) > > > -- > > Message: 1 > Date: Mon, 27 Nov 2017 12:04:04 +0100 > From: GIANMARCO BARTALINI > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] Pdb2gmx melts molecules due to bad distances > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > > Hello guys, I produced a system "protein + lipid membrane" using the > online > tool CHARMM-GUI. Since I need to use the Amber force field, I added the > Lipids17 force field inside Gromacs. The implementation should work fine, > since the conversion of an equilibrated structure produces a nice and > correct gro file. But when I try to convert the (not minimized) PDB file > that I get from CHARMM-GUI using pdb2gmx, I get a gro structure where many > lipid molecules are melted together (due to their bad distances). If I use > this structure for a minimization, the calculation stops due to bad > energies. Do you know how to solve this issue? > Thank you in advance, > > Gianmarco > > > -- > > Message: 2 > Date: Mon, 27 Nov 2017 17:47:36 +0530 > From: RAHUL SURESH > To: gmx-us...@gromacs.org > Subject: [gmx-users] Not enough memory. Failed to realloc > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > > Dear Users > > I am trying to carryout protein-metal interaction using charmm36 ff. > During > solvation *"gmx solvate -cp cuNew.gro -cs spc216.gro -p cu.top -o > solv.gro" > *i receive a error stating > > > > > > > > > *"Fatal error:Not enough memory. Failed to realloc 3094482528 bytes for > atoms_->atom,atoms_->atom=0(called from > file/home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/topology/atomsbuilder.cpp,line > 86)". * > I have enough space to carry out this simulation and I am using 2016 > version of gromacs. > > I couldnt diagonise the error exactly. Any help on this will be of great > use. > > Thank you > > -- > *Regards,* > *Rahul Suresh* > *Research Scholar* > *Bharathiar University* > *Coimbatore* > > > -- > > Message: 3 > Date: Mon, 27 Nov 2017 08:31:18 -0500 > From: Justin Lemkul > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] pH dependent simulation > Message-ID: > Content-Type: text/plain; charset=utf-8; format=flowed > > Thank you so much sir. > > On 11/26/17 11:09 PM, za...@tezu.ernet.in wrote: >> Hello Everyone >> >> I am trying to simulate a protein at two pH (7.4 and 9.0) using >> gromacs 5.1.4. The protein has no missing residues. Optimal pH range is >> 6.0 to 9.0 and pI of the protein is 11.4. It has 9 negatively and 17 >> positively charged residues. >> >> However upon predicting the pKa values using H++ server, I am getting >> the >> same pKa values for all the charged residues (at pH 7.4 and pH 9). And >> the >> total charge of +8e is also same at both pH 7.4 and 9.0. (Instead it >> should have different pKa values at pH 7 and 9). > > Why do you expect that? There are no amino acids with pKa in that range, > so nothing should change unless there are unique microenvironments that > shift canonical pKa values. As H++ has not detected any, likely your > protein behaves canonically. You can confirm your calculated pKa values > with another method, like PROPKA, to be sure. > > -Justin > >> Whether I am in the right direction or doing something wrong!!! >> >> Can anyone kindly suggest me how to proceed further? >> >> Any suggestion is appreciated. >> >
[gmx-users] -inter command
Dear Gromacs Users I have an query regarding gmx pdb2gmx -inter command. Do we use -inter command only for setting the protonation state of charged amino acids in order to perform simulation at different pH? Thank You Regards Zaved Hazarika Research Scholar Dept. Of Molecular Biology and Biotechnology, Tezpur University, 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. -- 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] -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 te
[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.
[gmx-users] -inter command
> Message: 3 > Date: Thu, 18 Jan 2018 07:39:39 -0500 > From: Justin Lemkul > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] -inter command > Message-ID: <0281054c-c062-90c3-2243-ef0f5f3ed...@vt.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > 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 Thank you so much Justin. 1. Yes you are correct. control here means default protonation state and in this case the system charge of +8e is neutralized. I didn't have any noncanonical pka values (at ph9). Checked with both H++ server and Propka. For ph 9, I have kept the charge of +8e. 2. Our experimental data suggests that at higher pH (9), the protein initiates unfolding. 3. I have taken the final structure (at 100ns) of both systems and superimposed it. I got a RMSD of 1.030 angstrom and no major structural change was observed. 4. We can consider to extend the simulation to visualize any change, if above things are correct. 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.
[gmx-users] -inter command
> 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 >> >> Thank you so much Justin. >> >> 1. Yes you are correct. control here means default protonation state and >> in this case the system charge of +8e is neutralized. I didn't have any >> noncanonical pka values (at ph9). Checked with both H++ server and >> Propka. >> For ph 9, I have kept the charge of +8e. >> >> 2. Our experimental data suggests that at higher pH (9), the protein >> initiates unfolding. >> >> 3. I have taken the final structure (at 100ns) of both systems and >> superimposed it. I got a RMSD of 1.030 angstrom and no major structural >> change was observed. >> >> 4. We can consider to extend the simulation to visualize any change, if >> above things are correct. > > There won't be one. Since the topologies are identical, you're running > the same simulation twice, and concluding that there are no major > variations between the two. You don't actually have any simulation that > you can claim is representing anything other than "pH 7," though pH > isn't really a thing in fixed-charge/fixed-topology MD. This is a > limitation of modeling something with fixed protonation states; it > doesn't necessarily reflect reality. A constant pH method might show > some results, but AFAIK this is not possible in GROMACS (though some > people do have custom code in old versions that might work). You may > want to consider a different program like AMBER or CHARMM that can do > these types of simulations. > > -Justin Thank You so much Justin. Can you provide the name and any link for older gromacs version? Thank You * * * 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.
[gmx-users] SDS initial setup
> 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: SDS initial setup (Dallas Warren) >2. Is there any difference with gromacs and other MD programs? > (??? (?)) >3. MDP define in GROMACS 2018 (Joshua Mitchell) >4. Cannot find position restraint file restraint.gro (Sailesh Bataju) > > > -- > > Message: 1 > Date: Mon, 22 Jan 2018 11:42:51 +1100 > From: Dallas Warren > To: GROMACS users > Subject: Re: [gmx-users] SDS initial setup > Message-ID: > > Content-Type: text/plain; charset="UTF-8" Thank you Justin and Dallas for your kind response. PBC comes into effect from the start of minimization step. As we apply it in the minim.mdp file as pbc = xyz. However in my case the SDS molecules appears to be outside during initial setup itself. Kindly correct me if I missed out something. However if that is the case, it might sounds vague but I am thinking why then we center the protein (eg and keep it 1 nm from the edge of the box to its center) during protein setup? Thank You Regards Zaved A visualisation to help see what is going on with the PBC and the > molecules https://twitter.com/dr_dbw/status/909559339366572032 > Catch ya, > > Dr. Dallas Warren > Drug Delivery, Disposition and Dynamics > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3052 > dallas.war...@monash.edu > - > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > On 19 January 2018 at 01:03, Andr? Farias de Moura > wrote: >> 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 * * * 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.
[gmx-users] Regarding Coulomb-14 Energy
Dear Gromacs Users I have simulated ricin in presence of GdmCl (1519 Gdm and 1519 Cl) with gromos54a7 ff. Simulations have been performed for 100ns each at 298K, 350K and 450K. The Average Coulomb-14 Energies are as follows: ricin in water (298K) : 3.42E+04 (positive value) ricin in water (350K) : 3.41E+04 (positive value) ricin in water (450K) : 3.40E+04 (positive value) ricin + GdmCl (298K) :-3.16E+06 (negative value) ricin + GdmCl (350K) : -3.17E+06 (negative value) ricin + GdmCl (450K) : -3.17E+06 (negative value) Can anyone suggest me why there is a (10 to the power 10) fold difference of average Coulomb-14 energy of ricin in presence of water and ricin in presence of GdmCl? Thank You Regards Zaved * * * 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] gromacs.org_gmx-users Digest, Vol 168, Issue 45
Dear Mark Thank you for the kind response. H with +0.418 charge and N with -0.845 charge is contributing towards coulomb 14 interaction. So what is the amount of interaction between one single H and N (3 bonds apart)? Kindly correct me if I am wrong. Here is my Gdm topology [ moleculetype ] ; name nrexcl GDM 3 [ atoms ] ; nrtype resnr residuatomcgnr charge MASS 1 C1GND C1 1 1.027 13.019 2 NT1GND N2 2 -0.845 14.0067 3 H1GND H3 2 0.418 1.008 4 H1GND H4 2 0.418 1.008 5 NT1GND N5 3 -0.845 14.0067 6 H1GND H6 3 0.418 1.008 7 H1GND H7 3 0.418 1.008 8 NT1GND N8 4 -0.845 14.0067 9 H1GND H9 4 0.418 1.008 10 H1GND H10 4 0.418 1.008 [ bonds ] 1 2 2 0.1340 1.0500e+07 1 5 2 0.1340 1.0500e+07 1 8 2 0.1340 1.0500e+07 2 3 2 0.1000 1.8700e+07 2 4 2 0.1000 1.8700e+07 5 6 2 0.1000 1.8700e+07 5 7 2 0.1000 1.8700e+07 8 9 2 0.1000 1.8700e+07 810 2 0.1000 1.8700e+07 [ angles ] 1 2 32 120.00 390.00 1 2 42 120.00 390.00 1 5 62 120.00 390.00 1 5 72 120.00 390.00 1 8 92 120.00 390.00 1 8102 120.00 390.00 3 2 42 120.00 445.00 6 5 72 120.00 445.00 9 8102 120.00 445.00 2 1 52 120.00 670.00 5 1 82 120.00 670.00 8 1 22 120.00 670.00 [ pairs ] ; aiaj funct c0 c1 2 6 1 0.00e+00 0.00e+00 2 7 1 0.00e+00 0.00e+00 2 9 1 0.00e+00 0.00e+00 210 1 0.00e+00 0.00e+00 5 3 1 0.00e+00 0.00e+00 5 4 1 0.00e+00 0.00e+00 5 9 1 0.00e+00 0.00e+00 510 1 0.00e+00 0.00e+00 8 3 1 0.00e+00 0.00e+00 8 4 1 0.00e+00 0.00e+00 8 6 1 0.00e+00 0.00e+00 8 7 1 0.00e+00 0.00e+00 [ dihedrals ] ; aiajakal gromos type 2 1 5 6 1 180.000 33.5 2 2 1 5 7 1 180.000 33.5 2 2 1 8 9 1 180.000 33.5 2 2 1 810 1 180.000 33.5 2 5 1 2 3 1 180.000 33.5 2 5 1 2 4 1 180.000 33.5 2 5 1 8 9 1 180.000 33.5 2 5 1 810 1 180.000 33.5 2 8 1 2 3 1 180.000 33.5 2 8 1 2 4 1 180.000 33.5 2 Thank you Regards Zaved Hazarika PhD Scholar Dept.of Molecular Biology and Biotechnology Tezpur University India > Hi, > > Presumably Gdm has atoms connected by three adjacent bonds that generally > have negative potential, and there's enough Gdm to make the total for the > system negative. It's generally a good idea to understand how the topology > you're using for Gdm works. > > Mark > > On Tue, Apr 10, 2018 at 2:23 PM wrote: > >> Dear Gromacs Users >> >> I have simulated ricin in presence of GdmCl (1519 Gdm and 1519 Cl) with >> gromos54a7 ff. Simulations have been performed for 100ns each at 298K, >> 350K and 450K. >> >> The Average Coulomb-14 Energies are as follows: >> >> ricin in water (298K) : 3.42E+04 (positive value) >> ricin in water (350K) : 3.41E+04 (positive value) >> ricin in water (450K) : 3.40E+04 (positive value) >> >> ricin + GdmCl (298K) :-3.16E+06 (negative value) >> ricin + GdmCl (350K) : -3.17E+06 (negative value) >> ricin + GdmCl (450K) : -3.17E+06 (negative value) >> >> Can anyone suggest me why there is a (10 to the power 10) fold >> difference >> of average Coulomb-14 energy of ricin in presence of water and ricin in >> presence of GdmCl? >> >> Thank You >> >> Regards >> >> Zaved * * * 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 b
[gmx-users] GPU Command
Dear Gromacs Users We have a GPU Server (Intel(R) Xeon(R) CPU E5-2609 v4 @ 1.70GHz, 16 cores) with 2 NVIDIA Tesla P100 (12GB) cards. What should be my final mdrun command so that it should utilize both the cards for the run? (As of now it detects both the cards, but auto selects only 1) As of now I am using the following command: gmx_mpi mdrun -v -deffnm run -gpu_id 0 1 I am using Gromacs 2016.4 version. For gromacs installation, used the following: CC=/usr/bin/mpicc F77=/usr/bin/f77 CXX=/usr/bin/mpicxx MPICC=/usr/bin/mpicc CMAKE_PREFIX_PATH=/soft/fftw337/lib cmake .. -DFFTWF_INCLUDE_DIR=/soft/fftw337/include -DFFTWF_LIBRARIES=/soft/fftw337/lib/libfftw3.so -DCMAKE_INSTALL_PREFIX=/soft/gmx164 -DGMX_X11=OFF -DCMAKE_CXX_COMPILER=/usr/bin/mpicxx -DCMAKE_C_COMPILER=/usr/bin/mpicc -DGMX_MPI=ON -DGMX_DOUBLE=OFF -DGMX_DEFAULT_SUFFIX=ON -DGMX_PREFER_STATIC_LIBS=ON -DGMX_SIMD=SSE2 -DGMX_SIMD=AVX2_256 -DGMX_USE_RDTSCP=OFF -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda Do I need to provide any other option (openMPI) while installing groamcs? Thank You Regards Zaved Hazarika PhD Scholar Dept.of Molecular Biology and Biotechnology Tezpur University Indi * * * 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.
[gmx-users] GPU Command
On Thu, Apr 12, 2018 at 4:47 PM wrote: > >> Dear Gromacs Users >> >> We have a GPU Server (Intel(R) Xeon(R) CPU E5-2609 v4 @ 1.70GHz, 16 >> cores) >> with 2 NVIDIA Tesla P100 (12GB) cards. >> >> What should be my final mdrun command so that it should utilize both the >> cards for the run? (As of now it detects both the cards, but auto >> selects >> only 1) >> >> As of now I am using the following command: >> >> gmx_mpi mdrun -v -deffnm run -gpu_id 0 1 >> > > You mentioned auto selection of GPU usage, but you are selecting the GPU > usage here, and you are requiring it to use only GPU 0. If you would look > at the examples in the user guide you would see how to use -gpu_id. If you > want permit mdrun to use its auto-selection, then don't use -gpu_id. > Thank you Mark for your kind response. However if I use the command without the gpu id (gmx_mpi mdrun -v -deffnm md), it still selects only 1 card, and the log file throws a message as follows: Using 1 MPI process Using 16 OpenMP threads 2 compatible GPUs are present, with IDs 0,1 1 GPU auto-selected for this run. Mapping of GPU ID to the 1 PP rank in this node: 0 NOTE: potentially sub-optimal launch configuration, gmx mdrun started with less PP MPI process per node than GPUs available. Each PP MPI process can use only one GPU, 1 GPU per node will be used. Will do PME sum in reciprocal space for electrostatic interactions. Kindly help. Thank You Regards Zaved Hazarika PhD Scholar Dept.of Molecular Biology and Biotechnology Tezpur University India > >> I am using Gromacs 2016.4 version. >> >> For gromacs installation, used the following: >> >> CC=/usr/bin/mpicc F77=/usr/bin/f77 CXX=/usr/bin/mpicxx >> MPICC=/usr/bin/mpicc CMAKE_PREFIX_PATH=/soft/fftw337/lib cmake .. >> -DFFTWF_INCLUDE_DIR=/soft/fftw337/include >> -DFFTWF_LIBRARIES=/soft/fftw337/lib/libfftw3.so >> -DCMAKE_INSTALL_PREFIX=/soft/gmx164 -DGMX_X11=OFF >> -DCMAKE_CXX_COMPILER=/usr/bin/mpicxx -DCMAKE_C_COMPILER=/usr/bin/mpicc >> -DGMX_MPI=ON -DGMX_DOUBLE=OFF -DGMX_DEFAULT_SUFFIX=ON >> -DGMX_PREFER_STATIC_LIBS=ON -DGMX_SIMD=SSE2 -DGMX_SIMD=AVX2_256 >> -DGMX_USE_RDTSCP=OFF -DGMX_GPU=ON >> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda >> > > Use only one GMX_SIMD setting - the one that matches the capabilities of > the CPU. > > >> Do I need to provide any other option (openMPI) while installing >> groamcs? >> > > You already chose to use your MPI library. > > Mark * * * 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.
[gmx-users] Regarding Coulomb-14 Energy
>> Dear Mark >> Thank you for the kind response. >> H with +0.418 charge and N with -0.845 charge is contributing towards coulomb 14 interaction. So what is the amount of interaction between one >> single H and N (3 bonds apart)? Kindly correct me if I am wrong. Thank you Justin for your kind response. I have also simulated ricin in presence of urea(1843 urea) with gromos54a7 ff. However with urea having similar kind of topology to that of Gdm, I am getting the Coulomb 14 with positive values. Why in this case the C14 is not having negative value? ricin + urea (298K): 3.41E+04 ricin + urea (350K): 3.41E+04 ricin + urea (450K): 3.40E+04 Urea Topology: [ UREA ] [ atoms ] OU OUREA-0.39000 0 CU CUREA 0.14200 0 N1U NUREA-0.54200 0 H11U H 0.33300 0 H12U H 0.33300 0 N2U NUREA-0.54200 0 H21U H 0.33300 0 H22U H 0.33300 0 [ bonds ] OUCUgb_44 CU N1Ugb_45 CU N2Ugb_45 N1U H11Ugb_2 N1U H12Ugb_2 N2U H21Ugb_2 N2U H22Ugb_2 Thank You Regards Zaved > Simply calculate it with Coulomb's Law and apply the 1-4 electrostatic scaling factor (if your force field uses one). > -Justin >> Here is my Gdm topology >> [ moleculetype ] >> ; name nrexcl >> GDM 3 >> [ atoms ] >> ; nrtype resnr residuatomcgnr charge MASS >> 1 C1GND C1 1 1.027 13.019 >> 2 NT1GND N2 2 -0.845 14.0067 3 H1GND H3 2 0.418 1.008 >> 4 H1GND H4 2 0.418 1.008 >> 5 NT1GND N5 3 -0.845 14.0067 6 H1GND H6 3 0.418 1.008 >> 7 H1GND H7 3 0.418 1.008 >> 8 NT1GND N8 4 -0.845 14.0067 9 H1GND H9 4 0.418 1.008 >> 10 H1GND H10 4 0.418 1.008 >>> Hi, >>> Presumably Gdm has atoms connected by three adjacent bonds that generally >>> have negative potential, and there's enough Gdm to make the total for the >>> system negative. It's generally a good idea to understand how the topology >>> you're using for Gdm works. >>> Mark >>> On Tue, Apr 10, 2018 at 2:23 PM wrote: >>>> Dear Gromacs Users >>>> I have simulated ricin in presence of GdmCl (1519 Gdm and 1519 Cl) with >>>> gromos54a7 ff. Simulations have been performed for 100ns each at 298K, >>>> 350K and 450K. >>>> The Average Coulomb-14 Energies are as follows: >>>> ricin in water (298K) : 3.42E+04 (positive value) >>>> ricin in water (350K) : 3.41E+04 (positive value) >>>> ricin in water (450K) : 3.40E+04 (positive value) >>>> ricin + GdmCl (298K) :-3.16E+06 (negative value) >>>> ricin + GdmCl (350K) : -3.17E+06 (negative value) >>>> ricin + GdmCl (450K) : -3.17E+06 (negative value) >>>> Can anyone suggest me why there is a (10 to the power 10) fold difference >>>> of average Coulomb-14 energy of ricin in presence of water and ricin in >>>> presence of GdmCl? >>>> Thank You >>>> Regards >>>> Zaved * * * 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.
[gmx-users] Coulomb-14 Energy
Dear Gromacs Users I have simulated a protein in presence of GdmCl (1519 Gdm and 1519 Cl) and Urea (urea 1843) with gromos54a7 ff for 100ns each. The Average Coulomb-14 Energies of protein in water, urea and GdmCl are: 3.42E+04, 3.41E+04 and -3.16E+06 respectively. The value of Coulomb-14 in case of protein in presence of water and protein in presence of urea are almost identical whereas it tends to be in different in case of GdmCl. And inspite of the fact that both urea and GdmCl have negative potential. How do we justify this? Thank You Regards Zaved Hazarika PhD Scholar Dept.of Molecular Biology and Biotechnology Tezpur University 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. -- 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] Coulomb-14 Energy
Thank you Mark and David for your kind responses. > Den 2018-04-24 kl. 15:49, skrev Mark Abraham: >> Hi, >> >> There is no physical meaning to this decomposition. There is nothing to >> justify. >> >> The total energies are different for each system, too. How would you >> justify that? They're just different systems with different >> compositions. >> I was thinking on the same line. Just wondering then why am I getting identical C-14 value in case of water and urea? Further does it mean that all other energy values except total has no meaning at all? Thank You > > The 1-4 energy has intramolecular contributions from the solvent as well > if it is larger than water. This is probably what you are seeing. > > Other than that Mark is right, there is only one energy. > >> Mark >> >> On Tue, Apr 24, 2018 at 1:35 PM wrote: >> >>> Dear Gromacs Users >>> >>> I have simulated a protein in presence of GdmCl (1519 Gdm and 1519 Cl) >>> and >>> Urea (urea 1843) with gromos54a7 ff for 100ns each. >>> >>> The Average Coulomb-14 Energies of protein in water, urea and GdmCl >>> are: >>> 3.42E+04, 3.41E+04 and -3.16E+06 respectively. >>> >>> The value of Coulomb-14 in case of protein in presence of water and >>> protein in presence of urea are almost identical whereas it tends to be >>> in >>> different in case of GdmCl. And inspite of the fact that both urea and >>> GdmCl have negative potential. >>> >>> How do we justify this? >>> >>> Thank You >>> >>> Regards >>> Zaved Hazarika >>> PhD Scholar >>> Dept.of Molecular Biology and Biotechnology >>> Tezpur University >>> 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. >>> -- >>> 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. >>> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > > * * * 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.
[gmx-users] ZnO Parameters
Dear Gromacs Users Can anyone provide me the parameters for Zinc Oxide (ZnO)? Thank You Regards Zaved Hazarika PhD Scholar Dept.of Molecular Biology and Biotechnology Tezpur University 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. -- 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] ZnO Parameters
> Message: 3 > Date: Fri, 6 Jul 2018 14:39:15 +0300 > From: ali akg?n > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] ZnO Parameters > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > > Hi, > > You can f?nd parameters on solid state books(for example kittel) Thank you for your kind suggestion. However I didn't found much info from it. > > Thank you. > > > 6 Tem 2018 Cum 13:09 tarihinde ?unu yazd?: > >> Dear Gromacs Users >> >> Can anyone provide me the parameters for Zinc Oxide (ZnO)? >> >> Thank You >> >> Regards >> Zaved Hazarika >> PhD Scholar >> Dept.of Molecular Biology and Biotechnology >> Tezpur University >> India Thank You Regards Zaved * * * 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.
[gmx-users] Number of glucose molcules
Dear Gromacs Users I have performed a simulation for native protein using gromacs. Now I want to add glucose molecules (in order to mimic diabetes condition) with eg. 240 mg/dL concentration. Can anyone help me with the calculation of the number of glucose molecules I need to add? The size of the simulation box is 10.98 * 10.98 * 10.98 nm. I appreciate any kind response. Regards Zaved * * * 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] Number of glucose molecules
> Message: 5 > Date: Sun, 9 Sep 2018 02:47:12 -0600 > From: Alex > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Number of glucose molcules > Message-ID: <870d39f7-471b-93f2-2444-6c432717f...@gmail.com> > Content-Type: text/plain; charset=utf-8; format=flowed Dear Alex Thank you so much for your kind words. We are not doing "medical research", we are trying to do and understand some basic science only. Are 11 molecules enough to bring about changes in the structure of human serum albumin in simulation; with 41000 water molecules in the simulation box. Can you kindly shed some light on it? Thank You Regards Zaved > People dear to my heart have diabetes, so... > > If you do not mind my asking, are you a high school student, or are you > actually a graduate student/postdoc? If it is the latter, please do the > humanity favor and send me the name of your advisor, because god forbid > medical research is done by people with gaps in knowledge of this > magnitude. I know I have been criticized on this forum for being less > than polite, but if any of us have a shred of integrity, we must do > something when medical research is concerned. > > If you are a secondary/high school student, the answer is below. > > The concentration is c = rho/mu, where rho is your density of 240mg/dL = > 2.4 g/L and mu = 180.156 g/mol is the molar mass of glucose. This yields > c = 0.0133M and c times the volume of the box is 11 molecules of glucose. > > Alex > > > On 9/9/2018 12:28 AM, za...@tezu.ernet.in wrote: >> Dear Gromacs Users >> >> I have performed a simulation for native protein using gromacs. >> Now I want to add glucose molecules (in order to mimic diabetes >> condition) >> with eg. 240 mg/dL concentration. >> Can anyone help me with the calculation of the number of glucose >> molecules >> I need to add? >> The size of the simulation box is 10.98 * 10.98 * 10.98 nm. >> >> I appreciate any kind response. >> >> Regards >> Zaved * * * 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] gromacs.org_gmx-users Digest, Vol 173, Issue 34
> Message: 1 > Date: Mon, 10 Sep 2018 22:16:03 -0600 > From: Alex > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Number of glucose molecules > Message-ID: <4050d74c-3628-a816-62cb-53160ceaa...@gmail.com> > Content-Type: text/plain; charset=utf-8; format=flowed > Dear Alex No I am not. I am a Research Student, pursuing from Dept.of Mol Bio and Biotechnology, Tezpur University, India. Thank You Zaved > Please answer my question. Are you a high school student, or do you > actually hold an academic degree from an accredited institution? > > Alex > >> Dear Alex >> >> Thank you so much for your kind words. >> >> We are not doing "medical research", we are trying to do and understand >> some basic science only. >> >> Are 11 molecules enough to bring about changes in the structure of human >> serum albumin in simulation; with 41000 water molecules in the >> simulation >> box. Can you kindly shed some light on it? >> >> Thank You >> >> Regards >> Zaved * * * 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.
[gmx-users] NVT LINCS Warning
Dear Gromacs Users I am trying to simulate glucose molecule and for that I am utilizing the gromos53a6carbo ff downloaded from http://www.gromacs.org/Downloads/User_contributions/Force_fields. After an successful energy minimization step, the NVT equilibration is throwing error messages and the equilibration is getting killed. Following is the error message (repeated no. of times): Step 0 Step 83, time 0.166 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000606, max 0.002103 (between atoms 16 and 17) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 16 17 46.60.1001 0.0998 0.1000 16 17 46.60.1001 0.0998 0.1000 16 17 46.60.1001 0.0998 0.1000 16 17 46.60.1001 0.0998 0.1000 16 17 46.60.1001 0.0998 0.1000 16 17 46.60.1001 0.0998 0.1000 16 17 46.60.1001 0.0998 0.1000 16 17 46.60.1001 0.0998 0.1000 N.B. I am using gromacs 5.1.4 version. Any kind suggestion/s will be appreciated. Thank You Regards Zaved Hazarika Research Scholar Dept. Of Molecular Biology and Biotechnology, Tezpur University, 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. -- 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] Regarding freezing of NP
Dear Users I am trying to simulate a spherical metal-oxide nanoparticle (NP) and the same NP with one protein of our interest. Can we freeze the NP during the NP-Protein simulation so as to keep the NP intact? Is it the right thing to do so? Any kind suggestion/s will be appreciated. Thank You Regards Zaved Hazarika Research Scholar Dept. Of Molecular Biology and Biotechnology, Tezpur University, 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. -- 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] Freezing Spherical Nanoparticle
Dear Users I am trying to simulate a spherical metal-oxide nanoparticle (NP) and the same NP with one protein of our interest. I wanted to know, is it advisable to freeze the NP during the NP-Protein simulation so as to keep the NP intact? Any kind suggestion/s will be appreciated. Thank You Regards Zaved Hazarika Research Scholar Dept. Of Molecular Biology and Biotechnology, Tezpur University, 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. -- 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] ramachandran plot
Dear Users Can anyone suggest me any available tool to analyze ramachandran plot timewise for a trajectory? Thank You Regards Zaved Hazarika Research Scholar Dept. Of Molecular Biology and Biotechnology, Tezpur University, 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. -- 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] ramachandran plot
> Message: 5 > Date: Wed, 9 Jan 2019 17:17:31 +0530 > From: Subhomoi Borkotoky > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] ramachandran plot > Message-ID: > > Content-Type: text/plain; charset="UTF-8" Hii Subhomoi Thank you so much for your suggestion. Regards Zaved > Hi Javed, > > I hope *gmx rama* will solve the issue. > > http://manual.gromacs.org/archive/5.0.4/programs/gmx-rama.html > > > Thanks & Regards, > -- > *Subhomoi Borkotoky, Ph. D.* > DBT Research Associate, > Kusuma School of Biological Sciences, > Indian Institute of Technology Delhi, > New Delhi-110016, > India. > > Alternate E-mail : subho...@yahoo.com > > > > > > On Wed, Jan 9, 2019 at 3:01 PM wrote: > >> Dear Users >> >> Can anyone suggest me any available tool to analyze ramachandran plot >> timewise for a trajectory? >> >> Thank You >> >> Regards >> Zaved Hazarika >> Research Scholar >> Dept. Of Molecular Biology and Biotechnology, >> Tezpur University, >> 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. -- 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] ramachandran plot
> Message: 4 > Date: Wed, 9 Jan 2019 11:59:31 +0100 > From: Tamas Hegedus > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] ramachandran plot > Message-ID: <563a0c65-532e-a47d-fdf7-5046a062c...@hegelab.org> > Content-Type: text/plain; charset=utf-8; format=flowed Hi Tamas Thank you so much for your suggestion. I will check that. Just to know one more thing, is there any program to know only number of residues in the allowed and favoured region in the output? Thank You > Hi, > > I use the python MDAnalysis packages for this. > > https://github.com/MDAnalysis/mdanalysis/issues/1335 > > https://www.mdanalysis.org/mdanalysis/documentation_pages/analysis/dihedrals.html > > Have a nice day, Tamas > > On 01/09/2019 10:30 AM, za...@tezu.ernet.in wrote: >> Dear Users >> >> Can anyone suggest me any available tool to analyze ramachandran plot >> timewise for a trajectory? >> >> Thank You >> >> Regards >> Zaved Hazarika >> Research Scholar >> Dept. Of Molecular Biology and Biotechnology, >> Tezpur University, >> 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. >> > > > -- > Tamas Hegedus, PhD > Senior Research Fellow > Department of Biophysics and Radiation Biology > Semmelweis University | phone: (36) 1-459 1500/60233 > Tuzolto utca 37-47| mailto:ta...@hegelab.org > Budapest, 1094, Hungary | http://www.hegelab.org > > > -- Regards Zaved Hazarika Research Scholar Dept. Of Molecular Biology and Biotechnology, Tezpur University, 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. -- 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] Protein coming out of simulation box.
Hello I had performed a 100ns protein simulation with gromacs 5.1.4. After the simulation I observed that the protein is coming out of the box. I have used the following commands to correct it: gmx_mpi trjconv -f md.xtc -s md.tpr -pbc mol -ur compact -center -o out.xtc gmx_mpi trjconv -f out.xtc -s md.tpr -dt 100 -o file.pdb Part of the protein is still out of the box (in the file.pdb). Please suggest. Thank You * * * 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.
[gmx-users] (no subject)
Hii Everyone I had performed a 100ns protein-ligand (docked complex) simulation with gromacs 5.1.4. The ligand in my case is hydrogen peroxide. I have removed the PBC effect and centered the protein. I have used the following commands: gmx_mpi trjconv -f md.xtc -s md.tpr -pbc nojump -o out.xtc gmx_mpi trjconv -f out.xtc -s md.tpr -pbc mol -center -o out_1.xtc I am analyzing the average distance between the protein and the ligand. I am getting a value of 3.2nm which is too high. Also in the out_1.xtc, after 10ns itself the ligand is moving all around the protein. Unable to understand why its happening!! Please suggest. Thank You Regards Z. Hazarika Research Scholar Tezpur University Tezpur, 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. -- 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] gromacs.org_gmx-users Digest, Vol 160, Issue 75
> 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: npt simulation error (Mohammad Zahidul Hossain Khan) >2. positioning molecule at desired location (Alex Mathew) >3. (no subject) (za...@tezu.ernet.in) >4. Re: (no subject) (RAHUL SURESH) >5. Re: Fwd: (saranya) >6. Re: gromacs.org_gmx-users Digest, Vol 160, Issue 74 (Naba) > > > -- > > Message: 1 > Date: Tue, 15 Aug 2017 18:22:03 -0700 > From: Mohammad Zahidul Hossain Khan > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] npt simulation error > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > > ; Dielectric constant (DC) for cut-off or DC of reaction field = > epsilon-r= 4 > > > On Tue, Aug 15, 2017 at 6:18 PM, Justin Lemkul wrote: > >> >> >> On 8/15/17 9:14 PM, Mohammad Zahidul Hossain Khan wrote: >> >>> Dear Sir >>> >>> I am trying to simulate protein_ligand complex using epsilon = 4 and it >>> is >>> giving the below error >>> >>> >> What is epsilon = 4? >> >> *2 particles communicated to PME rank 4 are more than 2/3 times the >> cut-off >>> out of the domain decomposition cell of their charge group in dimension >>> x* >>> >>> I have no idea how to solve this problem >>> >>> >> Have you Googled it, or gone to the GROMACS error page, where lots of >> advice lives? ;) >> >> -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. >> > > > > -- > > > *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics* > *Email: khan5...@vandals.uidaho.edu * > * Skype: parash.khan2* > *Cell: +12085967165* > > > -- > > Message: 2 > Date: Wed, 16 Aug 2017 09:48:59 +0530 > From: Alex Mathew > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] positioning molecule at desired location > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > > Dear all, > > I want to keep a water molecule at a particular position of a protein > channel. I need to pull this across the channel and observe the energy > diagram by PMF. can anyone tell me how I can keep water molecules at a > particular position. > > thank you. > > > -- > > Message: 3 > Date: Wed, 16 Aug 2017 10:11:44 +0530 > From: za...@tezu.ernet.in > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] (no subject) > Message-ID: > <49c5c50c859cae2587445e0f293eae63.squir...@webmail.tezu.ernet.in> > Content-Type: text/plain;charset=utf-8 > > Hii Everyone > > I had performed a 100ns protein-ligand (docked complex) simulation with > gromacs 5.1.4. > > The ligand in my case is hydrogen peroxide. > > I have removed the PBC effect and centered the protein. > > I have used the following commands: > > gmx_mpi trjconv -f md.xtc -s md.tpr -pbc nojump -o out.xtc > > gmx_mpi trjconv -f out.xtc -s md.tpr -pbc mol -center -o out_1.xtc > > I am analyzing the average distance between the protein and the ligand. I > am getting a value of 3.2nm which is too high. > > Also in the out_1.xtc, after 10ns itself the ligand is moving all around > the protein. > > Unable to understand why its happening!! > > Please suggest. > > Thank You > > Regards > > Z. Hazarika > Research Scholar > Tezpur University > Tezpur, 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 > deli
[gmx-users] restrained md_coordinate issue
Hello Everyone I have simulated a protein - ligand complex with gromacs 5.1.4 for 100ns. I have restrained the position of the ligand ( which in my case is hydrogen peroxide). Applied following commands for correcting pbc: gmx_mpi trjconv -f md.xtc -s md.tpr -pbc -nojump -o file1.xtc gmx_mpi trjconv -f file1.xtc -pbc mol -center -o file2.xtc After correcting the pbc effect, the coordinates of my ligand changes throughout the simulation (which should not be the case). I would also like to mention that the coordinates of my ligand in the md.xtc is fixed. But after applying above 2 commands, the ligand coordinates changes. Can't understand what's wrong!!! Any suggestion is appreciated. Thank You Regards Zaved * * * 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] gromacs.org_gmx-users Digest, Vol 162, Issue 7
> 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. Charges and Antechamber (ABEL Stephane)
>2. Re: peptide ligand (farial tavakoli)
>3. Re: grompp very slow generating .tpr when excluded bonded
> neighbours is large (Mark Abraham)
>4. Re: Charges and Antechamber (Jo?o Henriques)
>5. checking simulation progress (Bukunmi Akinwunmi)
>
>
> --
>
> Message: 1
> Date: Tue, 3 Oct 2017 15:10:33 +
> From: ABEL Stephane
> To: "gromacs.org_gmx-users@maillist.sys.kth.se"
>
> Subject: [gmx-users] Charges and Antechamber
> Message-ID:
> <3e39b768bb199548ab18f7289e7534af38818...@exdag0-b0.intra.cea.fr>
> Content-Type: text/plain; charset="us-ascii"
>
> HI
>
> It is quite easy to derive RESP charges and use them with GROMACS. You
> could follow the steps
>
> 1) Build a pdb file of your molecule/modified residue
> 2) Use the web server pyRED
> (http://upjv.q4md-forcefieldtools.org/REDServer-Development/) and derive
> the RESP charges. The webserver will also give you all the necessary
> parameters of the ff (mol2 file, atom types, (non)bonded parameters)
> 3) Use these parameters to construct a rtp file for GROMACS for a given
> force field
> 4) and finally use pdb2gmx with the pdb file to obtain the itp file.
>
> That's all
>
> Good luck
>
>
> --
>
> Message: 2
> Date: Tue, 3 Oct 2017 15:13:58 + (UTC)
> From: farial tavakoli
> To:
> Subject: Re: [gmx-users] peptide ligand
> Message-ID: <1201432437.876905.1507043638...@mail.yahoo.com>
> Content-Type: text/plain; charset=UTF-8
>
> blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
> #715FFA solid !important; padding-left:1ex !important;
> background-color:white !important; } Thanks alot for your advxe
> I would really appreciate if you advice me more to split protein and
> ligand in index file, I saw the index help , but couldnt find out how
> should I use ? ?splitch? nr ? script to split them.?
> With best regardsFarial
gmx make_ndx -f em.gro -o index.ndx
then select protein ( in your case it will contain both the protein and
the peptide) and your ligand.
press q (save it)
now assemble your nvt tpr file using grompp ( pass here -n index.ndx)
It is explained very nicely in gromacs tutorial Protein - Ligand
(Equilibration section)
thank you
>
> Sent from Yahoo Mail for iPhone
>
>
> On Tuesday, October 3, 2017, 4:51 PM, Justin Lemkul
> wrote:
>
>
>
> On 10/3/17 9:17 AM, ?farial tavakoli? ? wrote:
>> Dear Justin
>>
>> Thank you so much for your reply.
>> You mean , I should generate a topology file for my complex instead of
>> creating topology for each of them separately ?
>>
>
> As long as the protein and peptide ligand are denoted as being in
> separate chains (different chain ID or use of TER in the PDB file), then
> pdb2gmx will do everything for you.
>
> -Justin
>
>>
>>
>>
>> *From:* Justin Lemkul
>> *To:* gmx-us...@gromacs.org; ?farial tavakoli? ?
>>
>> *Sent:* Tuesday, 3 October 2017, 16:35:49
>> *Subject:* Re: [gmx-users] peptide ligand
>>
>>
>>
>> On 10/3/17 4:26 AM, ?farial tavakoli? ? wrote:
>> > Dear GROMACS users
>> > I need to run a MD on my Protein-peptide ligand complex in GROMACS.
>> I generated my ligand topology by gromose96 54a7 ff ( [moleculetypes]
>> was Protein_chain_B) and converted it to .itp file to string it in
>> Protein.top file, then, added Protein_chain_B in [ molecules ]
>> directive to create one topology file for my complex. Created newbox
>> and solvate.
>>
>> You shouldn't have to do any topology manipulation. pdb2gmx handles
>> multiple
>> chains natively without any additional effort on your part.
>>
>> -Justin
>>
>>
>> > But when I gave this command:gmx grompp -f em_real.mdp -c
>> solv_ions.gro -p topol.top -o em.tpr
>> >
>> > I faced to this error:
>> >
>> > Group Protein_chain_B referenced in the .mdb file was not found in
>> the index file. Group names must match either [moleculetype] names or
>> custom index group names, in which case you must supply an index file
>> to the '-n' option
>> > of grompp.
>> >
>> > In spite of , my ligand [ moleculetypes ] in the ligand.itp file is
>> Protein_chain_B , but GROMACS gives error.
>> > Would you please advice me how can I solve this problem?
>> >
>> > Best
>> > Farial
>>
[gmx-users] Lipid Simulation Analysis
Hello What kind of analysis can we perform for a lipid bilayer simulation? And which are the tools available in gromacs to analyse bilayer simulation? Thank You Regards Z. Hazarika Research Scholar Tezpur University Tezpur ___ 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] Lipid Simulation Analysis
Hello Nikhil Maroli Basically I am new to lipid bilayer simulation. As of now I don't have any particular objective. I am trying to learn lipid bilayer simulation. Any suggestion would be great. How can I check the stability of my simulated bilayer? ___ 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.
