[gmx-users] Reg Replica exchange Molecular dynamics
Dear Justin Thank you For your previous reply I would like to do REMD (Replica exchange MD) in gromacs I am very happy if you paste tutorial for REMD, Targeted MD , Constraint MD and Non Equilibrium MD as you develop the Tutorial for other Methods in your web page. Your Tutorial is so clear and understandable . So May I expect Tutorial for aforesaid Technique in nutshell manner? It will be highly helpful So i Humbly request you to Put Tutorial Thanks In Advance -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Reg Replica exchange Molecular dynamics
On 1/14/14, 7:29 AM, vidhya sankar wrote: Dear Justin Thank you For your previous reply I would like to do REMD (Replica exchange MD) in gromacs I am very happy if you paste tutorial for REMD, Targeted MD , Constraint MD and Non Equilibrium MD as you develop the Tutorial for other Methods in your web page. Your Tutorial is so clear and understandable . So May I expect Tutorial for aforesaid Technique in nutshell manner? No, sorry. I only develop tutorials when I have a need for the technique myself or if I find myself with an abundance of free time, neither of which is currently the case. Development of a tutorial usually takes weeks of effort and many hours spent on revision and subsequent upkeep. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] How much should epsilon-r be set?
Dear gmx-users, I use GMX to simulate a protein 700 peptide long with a ligand. The protein-ligand complex is put in a box with explicit water. I use AMBER99 force field. The epsilon-r was set with the default value 1, with coulombtype=PME. The problem is, the energy generated from .xtc file using g_energy showed large difference between coulomb energy and VDW potential energy. For example, I calculate the energy between the ligand and the protein, which were, Coul-SR=-406.172, LJ-SR=-115.504. We thought during the protein-ligand interaction, the coulomb energy and VDW energy should have similar values. But the results seemed to indicate that coulomb force had a much more important impact on the interaction. Is there any problem I set the epsilon-r=1? Should I change it larger to weaken the coulomb impact? The ligand locates in the active pocket of the protein, which is a hydrophilic environment and will attract several water molecules during MD. Thanks a lot! Qing Li -- 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] Computing melting point
Hello everyone! I would like to compute the melting point of a drug crystalline system. In the literature, there exist a good number of methods to do so! Among them, I read Gibbs-Duhem integration technique in which one needs to provide a reference coexistence of solid/liquid. I read some articles in which they studied the melting point of water and also some ionic crystals. But I would like to know whether you can suggest me some more materials to read to find some ideas how to choose the reference structure for drug crystals? At the end, I would like to perform this simulation using gromacs. So if you think there are other methods which are more straight forward, would be great to let me know. Best G. -- 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] errors with charmm36 ?
Hi Justin and Hubert:
Many thanks for your kind pointing out. Are you using the new version of
CHARMM36? I am using the one from here:
http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36_gmx_format_sep13.tgz
I opened the merged.rtp file within the charmm36.ff file and found:
[ POPC ]
[ atoms ]
N NTL -0.600 0
C12 CTL2 -0.100 1
H12AHL0.250 2
H12BHL0.250 3
C13 CTL5 -0.350 4
H13AHL0.250 5
H13BHL0.250 6
H13CHL0.250 7
C14 CTL5 -0.350 8
H14AHL0.250 9
H14BHL0.250 10
H14CHL0.250 11
C15 CTL5 -0.350 12
H15AHL0.250 13
H15BHL0.250 14
H15CHL0.250 15
C11 CTL2 -0.080 16
H11A HAL20.090 17
H11B HAL20.090 18
PPL1.500 19
O13 O2L -0.780 20
Here is the information in my system.pdb file:
CRYST1 68.504 68.504 100.000 90.00 90.00 90.00 P 1 1
ATOM 1 N POPCA 1 -23.882 12.660 22.550 1.00-19.80 MEMB
ATOM 2 C12 POPCA 1 -23.575 13.505 21.320 1.00-19.52 MEMB
ATOM 3 H12A POPCA 1 -22.869 12.963 20.709 1.00 0.00 MEMB
ATOM 4 H12B POPCA 1 -23.032 14.387 21.628 1.00 0.00 MEMB
ATOM 5 C13 POPCA 1 -24.769 11.520 22.190 1.00-20.41 MEMB
ATOM 6 H13A POPCA 1 -24.241 10.891 21.490 1.00 0.00 MEMB
ATOM 7 H13B POPCA 1 -25.124 11.119 23.128 1.00 0.00 MEMB
ATOM 8 H13C POPCA 1 -25.638 11.934 21.700 1.00 0.00 MEMB
ATOM 9 C14 POPCA 1 -22.673 12.210 23.289 1.00-19.18 MEMB
ATOM 10 H14A POPCA 1 -23.025 11.888 24.257 1.00 0.00 MEMB
ATOM 11 H14B POPCA 1 -22.117 11.419 22.806 1.00 0.00 MEMB
ATOM 12 H14C POPCA 1 -21.935 12.981 23.456 1.00 0.00 MEMB
ATOM 13 C15 POPCA 1 -24.601 13.537 23.461 1.00-18.70 MEMB
ATOM 14 H15A POPCA 1 -24.979 13.080 24.364 1.00 0.00 MEMB
ATOM 15 H15B POPCA 1 -25.469 13.977 22.992 1.00 0.00 MEMB
ATOM 16 H15C POPCA 1 -23.953 14.351 23.749 1.00 0.00 MEMB
ATOM 17 C11 POPCA 1 -24.755 13.765 20.262 1.00-20.80 MEMB
ATOM 18 H11A POPCA 1 -24.458 14.498 19.482 1.00 0.00 MEMB
ATOM 19 H11B POPCA 1 -25.669 14.146 20.766 1.00 0.00 MEMB
ATOM 20 P POPCA 1 -24.213 11.984 18.366 1.00-18.20 MEMB
ATOM 21 O13 POPCA 1 -24.848 10.757 17.832 1.00-17.27 MEMB
ATOM 22 O14 POPCA 1 -22.825 11.910 18.814 1.00-18.67 MEMB
ATOM 23 O12 POPCA 1 -25.078 12.575 19.526 1.00-17.51 MEMB
The line 3 in merged.rtp and my .pdb file are H12a. The order seems to
be all right
thank you very much.
Albert
On 01/14/2014 02:55 PM, hubert santuz wrote:
Hi,
I just came across this issue a few days ago (with charmm-gui also).
In fact, atoms C13, C14 and C15 should be just after the C12 atoms in
the pdb (to match the itp file).
Here a piece of code that I used to retrieve the good order for all
POPC molecules in your gro file (on unix platform) :
for i in `grep POPC C13 yourfile.gro --line-number | awk -F:
'{print $1}'`
do
j=$((i-3))
(echo ${i}m${j}; echo w; echo q ) | ed yourfile.gro
done
Basically, ed is used to move each line POPC C13, 3 lines above. (6
lines for C14 and 9 lines for C15).
Beware also that a certain number of atom's name are wrong also :
0C21 (charmm-gui file) -- 'C210' (itp file)
1H10 -- 'H101'
etc.
In this case, 'sed' is a great tool ;)
Cheers,
Hubert
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Re: [gmx-users] Polymer Relaxation Issue
Justin, Thanks for your reply to this and my previous post! I looked at my .mdp and found the following line actually restrict the atom positions. ; VARIOUS PREPROCESSING OPTIONS define = -DPOSRES I have another question on dihedral angle parameter definition. I will post in a separate message. I would appreciate it if you can help. Best Regards, decaiyu -- View this message in context: http://gromacs.5086.x6.nabble.com/Polymer-Relaxation-Issue-tp5013734p5013753.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] errors with charmm36 ?
On 01/14/2014 04:12 PM, Justin Lemkul wrote: The .top is what matters, and your topology showed a clearly different order of atoms. Check the correspondence of the output configuration from pdb2gmx and the .top file. Inputs and .rtp entries are irrelevant once pdb2gmx is done working. -Justin Hi Justin: Many thanks for your helpful advices. The problem solved now. I some kind of mix the old c36 FF with the new one. I just update it in my system few days ago. thanks again for sugguestions. best Albert -- 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] errors with charmm36 ?
I use this charmm36 (http://www.gromacs.org/@api/deki/files/184/=charmm36.ff_4.5.4_ref.tgz, from Piggot et al, 2012, JCTC) which have slight differences in the order and in the name of few atoms compared to the one you used. So, everything I said concern only this version ;) Cheers, Hubert Le 14/01/2014 16:42, Albert a écrit : On 01/14/2014 04:12 PM, Justin Lemkul wrote: The .top is what matters, and your topology showed a clearly different order of atoms. Check the correspondence of the output configuration from pdb2gmx and the .top file. Inputs and .rtp entries are irrelevant once pdb2gmx is done working. -Justin Hi Justin: Many thanks for your helpful advices. The problem solved now. I some kind of mix the old c36 FF with the new one. I just update it in my system few days ago. thanks again for sugguestions. best Albert -- Hubert SANTUZ Equipe DSIMB UMR-S 665, INSERM-Paris Diderot, INTS 6 rue Alexandre Cabanel 75015 Paris Tel : 01 44 49 31 53 -- 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] errors with charmm36 ?
On 1/14/14, 10:58 AM, hubert santuz wrote: I use this charmm36 (http://www.gromacs.org/@api/deki/files/184/=charmm36.ff_4.5.4_ref.tgz, from Piggot et al, 2012, JCTC) which have slight differences in the order and in the name of few atoms compared to the one you used. So, everything I said concern only this version ;) I think it is probably worth emphasizing a point I have made previously, because I suspect there may be some confusion among the users out there. The tarball that can be downloaded from the website contains updated parameters for CHARMM36 lipids ONLY. The parameters in that distribution have outdated CHARMM22+CMAP parameters for proteins and CHARMM27 for nucleic acids (i.e. the files distributed as charmm27.ff in Gromacs). Users should not be led to believe that this tarball contains the full CHARMM36 force field, which is a different entity, available only from the MacKerell lab (note we will be uploading a new tarball soon that has updated parameters for CGenFF 2b8). -Justin Cheers, Hubert Le 14/01/2014 16:42, Albert a écrit : On 01/14/2014 04:12 PM, Justin Lemkul wrote: The .top is what matters, and your topology showed a clearly different order of atoms. Check the correspondence of the output configuration from pdb2gmx and the .top file. Inputs and .rtp entries are irrelevant once pdb2gmx is done working. -Justin Hi Justin: Many thanks for your helpful advices. The problem solved now. I some kind of mix the old c36 FF with the new one. I just update it in my system few days ago. thanks again for sugguestions. best Albert -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Reg Replica exchange Molecular dynamics
Google knows about two GROMACS REMD tutorials, by the way! Mark On Tue, Jan 14, 2014 at 1:30 PM, vidhya sankar scvsankar_...@yahoo.comwrote: Dear Justin Thank you For your previous reply I would like to do REMD (Replica exchange MD) in gromacs I am very happy if you paste tutorial for REMD, Targeted MD , Constraint MD and Non Equilibrium MD as you develop the Tutorial for other Methods in your web page. Your Tutorial is so clear and understandable . So May I expect Tutorial for aforesaid Technique in nutshell manner? It will be highly helpful So i Humbly request you to Put Tutorial Thanks In Advance -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] errors with charmm36 ?
It is good to know that the c36 and CGenFF is actively update. I just noticed that this new version c36 no longer contains classic TII3P water models: 1: TIP3P TIP 3-point, recommended, by default uses CHARMM TIP3 with LJ on H 2: TIP4P TIP 4-point 3: TIP5P TIP 5-point 4: SPC simple point charge 5: SPC/E extended simple point charge 6: None So in priciple, we have to use CHARMM TIP3P model, is it correct? I am always wondering, would it be better if there is a tool that could convert the output from paramchem websever into a single ligand.itp file? The parachem website can export the results including all known information from CGenFF related to target ligand. In such compelte output file, it contains all necessary information for a ligand parameters and toplogy thank you very much Albert On 01/14/2014 05:14 PM, Justin Lemkul wrote: I think it is probably worth emphasizing a point I have made previously, because I suspect there may be some confusion among the users out there. The tarball that can be downloaded from the website contains updated parameters for CHARMM36 lipids ONLY. The parameters in that distribution have outdated CHARMM22+CMAP parameters for proteins and CHARMM27 for nucleic acids (i.e. the files distributed as charmm27.ff in Gromacs). Users should not be led to believe that this tarball contains the full CHARMM36 force field, which is a different entity, available only from the MacKerell lab (note we will be uploading a new tarball soon that has updated parameters for CGenFF 2b8). -Justin -- 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] errors with charmm36 ?
On 1/14/14, 11:38 AM, Albert wrote: It is good to know that the c36 and CGenFF is actively update. I just noticed that this new version c36 no longer contains classic TII3P water models: 1: TIP3P TIP 3-point, recommended, by default uses CHARMM TIP3 with LJ on H 2: TIP4P TIP 4-point 3: TIP5P TIP 5-point 4: SPC simple point charge 5: SPC/E extended simple point charge 6: None So in priciple, we have to use CHARMM TIP3P model, is it correct? You can use TIP3P without LJ terms on H atoms by making use of a define statement in the .mdp file; see ffnonbonded.itp for details. We promote the use of the TIP3P model with LJ on H because it makes a huge difference for some systems, especially lipids. Proteins are less sensitive to differences between the two TIP3P variants. But strictly speaking, with CHARMM, we always use the TIP3P model with LJ terms on H atoms since that's what we do during parametrization. I am always wondering, would it be better if there is a tool that could convert the output from paramchem websever into a single ligand.itp file? The parachem website can export the results including all known information from CGenFF related to target ligand. In such compelte output file, it contains all necessary information for a ligand parameters and toplogy We're working on that. Seamless integration between the different software packages is a goal we have. For now, you'll have to hack the output a bit to make it syntactically correct. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] errors with charmm36 ?
I would just like to also re-iterate the point made by Justin. The conversion of the lipid parameters into GROMACS format was done before there were published updates to other parts of the CHARMM force field and so it is only the lipids which are the CHARMM36 parameters. Regarding the choice of TIP3P water to use, further details regarding the impact of the water model upon lipid membranes (which can be large) and proteins (which was suggested to be minimal) can be seen in the following papers: Lipids: http://pubs.acs.org/doi/abs/10.1021/ct3003157 Proteins: http://pubs.acs.org/doi/abs/10.1021/ct900549r Cheers Tom Justin Lemkul wrote: On 1/14/14, 10:58 AM, hubert santuz wrote: I use this charmm36 (http://www.gromacs.org/@api/deki/files/184/=charmm36.ff_4.5.4_ref.tgz, from Piggot et al, 2012, JCTC) which have slight differences in the order and in the name of few atoms compared to the one you used. So, everything I said concern only this version ;) I think it is probably worth emphasizing a point I have made previously, because I suspect there may be some confusion among the users out there. The tarball that can be downloaded from the website contains updated parameters for CHARMM36 lipids ONLY. The parameters in that distribution have outdated CHARMM22+CMAP parameters for proteins and CHARMM27 for nucleic acids (i.e. the files distributed as charmm27.ff in Gromacs). Users should not be led to believe that this tarball contains the full CHARMM36 force field, which is a different entity, available only from the MacKerell lab (note we will be uploading a new tarball soon that has updated parameters for CGenFF 2b8). -Justin Cheers, Hubert Le 14/01/2014 16:42, Albert a écrit : On 01/14/2014 04:12 PM, Justin Lemkul wrote: The .top is what matters, and your topology showed a clearly different order of atoms. Check the correspondence of the output configuration from pdb2gmx and the .top file. Inputs and .rtp entries are irrelevant once pdb2gmx is done working. -Justin Hi Justin: Many thanks for your helpful advices. The problem solved now. I some kind of mix the old c36 FF with the new one. I just update it in my system few days ago. thanks again for sugguestions. best Albert -- Dr Thomas Piggot University of Southampton, UK. -- 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] name problem
I think you can't. People have asked similar questions before. You need to rename the lipids yourself to 3 letter names e.g. POC and POG. Hello: I found a problem of lipids name when I use editconf each time. My lipids name are: POPC and POPG. When I run command: editconf -f em.gro -o em.pdb the name of my lipids for both POPC and POPG are POP. I am just wondering how can we solve this problem by exporting the full name of lipids? thank you very much Albert -- 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] name problem
On 1/14/14, 12:37 PM, Albert wrote: Hello: I found a problem of lipids name when I use editconf each time. My lipids name are: POPC and POPG. When I run command: editconf -f em.gro -o em.pdb the name of my lipids for both POPC and POPG are POP. I am just wondering how can we solve this problem by exporting the full name of lipids? editconf only writes 3 characters for PDB residue names, per standard format. The same is true with other Gromacs programs like trjconv. Either stick with .gro format, which permits 4 characters, or write a script to post-process the output. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Computing melting point
Lindemann criterion might be easier. See For example, * Materials science: Melting from within Nature 413, 582-583 (11 October 2001) | doi:10.1038/35098169 Robert W. Cahn On 14 January 2014 15:35, Golshan Hejazi golshan.hej...@yahoo.com wrote: Hello everyone! I would like to compute the melting point of a drug crystalline system. In the literature, there exist a good number of methods to do so! Among them, I read Gibbs-Duhem integration technique in which one needs to provide a reference coexistence of solid/liquid. I read some articles in which they studied the melting point of water and also some ionic crystals. But I would like to know whether you can suggest me some more materials to read to find some ideas how to choose the reference structure for drug crystals? At the end, I would like to perform this simulation using gromacs. So if you think there are other methods which are more straight forward, would be great to let me know. Best G. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] how to modify the shake algorithm
Dear Gromacs user/developer, I want to modify the Shake program in gromacs 4.x to constrain the reaction coordinate to a fixed value, and then get the corresponding constrain force applied. Does anyone could help me about which file i need modify, and how to modify it? Any help will be appreciated. Thanks. yours sincerely, Hu -- 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] About membrane protein
Justin Lemkul wrote You will have to position the protein differently if it is oriented asymmetrically with respect the the membrane. The same principles apply, but box vectors will certainly be different, as will the editconf command. -Justin - https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request@ . Thanks Justin! It Is asymmetric because the protein consists of a outer-membrane domain and a transmembrane helix. I placed the protein asymmetrically to let the transmembrane helix in the middle of the bilayer (dppc128) and adjusted the size of box. I confirmed that by checking the coordinates in the system.gro and system_inflated.gro. But after that step, after I did grompp -f minim.mdp -c system_inflated.gro -o confout.tpr -maxwarn 1 and mdrun -deffnm confout -nt 1 the coordinates of protein were dramatically changed, i.e. the protein was totally away from the bilayer. I think that should be something wrong, but cannot find it. -- View this message in context: http://gromacs.5086.x6.nabble.com/About-membrane-protein-tp5013733p5013766.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Polymer Dihedral Angle Definition
Dear All, When I look at the dihedral angle definition (see below) for gromos43a1 force field, most equilibrium angles are either 180 or 0 degrees. I assume that the second number represent the strength of dihedral angle term and the third one is the power. How do I define the gd term involving a tetrahedral structure, such as C-C-N-(C3). The equilibrium angle here is not 180 or 0 degree. How do I decide the value for the second and third term? ; ICP(H)[N] CP[N] PD[N] NP[N] ; #define gd_1180.000 5.86 2 ; -C-C- 1.4 ; #define gd_2180.000 7.11 2 ; -C-OA- (at ring) 1.7 ; Best Regards, decaiyu -- View this message in context: http://gromacs.5086.x6.nabble.com/Polymer-Dihedral-Angle-Definition-tp5013768.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] About membrane protein
On 1/14/14, 2:13 PM, paulxie wrote: Justin Lemkul wrote You will have to position the protein differently if it is oriented asymmetrically with respect the the membrane. The same principles apply, but box vectors will certainly be different, as will the editconf command. -Justin - https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request@ . Thanks Justin! It Is asymmetric because the protein consists of a outer-membrane domain and a transmembrane helix. I placed the protein asymmetrically to let the transmembrane helix in the middle of the bilayer (dppc128) and adjusted the size of box. I confirmed that by checking the coordinates in the system.gro and system_inflated.gro. But after that step, after I did grompp -f minim.mdp -c system_inflated.gro -o confout.tpr -maxwarn 1 and mdrun -deffnm confout -nt 1 the coordinates of protein were dramatically changed, i.e. the protein was totally away from the bilayer. I think that should be something wrong, but cannot find it. Without seeing your exact commands, neither can anyone else. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] How to define pull-init for two pull groups
Dear gmx-users, Thanks for the nice reply. I have corrected the pull code as: ; Pull code pull= umbrella pull_geometry = position ; pull_dim= N N Y pull_start = yes; define initial COM distance 0 pull_ngroups= 2 pull_group0 = cbilayer ; center of carbon's of bilayer pull_group1 = phosup ; phosphate atom of 16th PEPC in top pull_pbcatom1 = 0 pull_vec1 = 0.0 0.0 -1.0 pull_init1 = 0 0 0 pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_group2 = phoslow ; phosphate atom of 56th PEPC in bottom pull_pbcatom2 = 0 pull_vec2 = 0.0 0.0 1.0 pull_init2 = 0 0 0 pull_rate2 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k2 = 1000 ; kJ mol^-1 nm^-2 Now, after extracting trajectory frames and measuring the distances between COM distances between two pull groups and a reference group, I found that values of summary_distances.dat are first decreasing through roughly half of the frames and then start increasing till final frame. The snapshots are also matching the output. If this is right for a lipid crossing through bilayer then in order to generate starting configurations at windows spacing of 0.06 nm I ran the script (setup-umbrella.py) link provided in tutorial. But, the output file (caught_output.txt) which contain the list of initial frames with distances select only frames after half of the times frames. i.e If I provide a .dat file corresponding to 400 time frames it produces the list of frames at a desired spacing excluding the frames where distance between reference and pull group is decreasing . I got : Creating frame-specific output for files: run-umbrella.sh frame distd_dist 0 3.082NA 6 3.137 0.055 222 3.215 0.078 224 3.272 0.057 228 3.320 0.049 230 3.380 0.060 231 3.427 0.047 237 3.495 0.068 239 3.557 0.062 240 3.619 0.062 242 3.720 0.102 257 3.781 0.061 271 3.835 0.053 272 3.894 0.059 283 3.935 0.041 286 4.010 0.075 288 4.063 0.053 299 4.113 0.049 300 4.188 0.075 302 4.243 0.055 305 4.303 0.060 311 4.397 0.094 312 4.431 0.034 If this is case, how it will generate a sufficient overlap between adjacent windows ? Also, script works only for single lipid pulling out of a layer. It is possible to use it for two lipids simultaneously crossing the bilayer in different directions. Thanks and Regards, Rini gmx-us...@gromacs.org On 1/13/14, 7:40 PM, Rini Gupta wrote: Dear gmx-users, I want to calculate Potential of Mean Force (PMF) of a lipid in a bilayer by umbrella sampling method using coarse grain molecular dynamics simulations. My simulation system consists of 76 (PEPC and GDPE lipids mixture), 2495 water molecules and 16 other molecules which are acting as a surface attached to this bilayer system. In order to generate starting structures for the pulling simulations, after minimization, I have equilibrated the system for 25 ns under NVT ensemble followed by 25 ns NPT run with position restraints applied to both lipids and surface molecules. Following this, I have ran production simulations under NPT ensemble for another 25 ns. During production phase, position restraints were removed from all lipids except surface molecules. I want to calculate PMF for pulling out two lipids simultaneously one in top and one in bottom layer of this system. Following Justin tutorial, I understand that I need to define two pull groups and one reference group for my problem. For this, I have chosen all carbon's of lipid bilayer as reference group and Phosphate atom of two lipids which are placed in top and bottom layers respectively, as pull group1=phosup and pull group2 =phoslow My problem is how to define pull-init for two pull groups: I have to directly place the initial coordinates of two selected lipids as pull-init or first I need to assume that bilayer center is shifted to (0,0,0 ) and then put initial cordinates as pull-init. Please let me know if anything is wrong here. Following second approach, I have used the following grompp.mdp file for pulling simulation: ; Pull code pull= umbrella pull_geometry = position ; pull_dim= N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups= 2 pull_group0 = cbilayer ; center of carbon's of bilayer pull_group1 = phosup ; phosphate atom of 16th PEPC in top pull_pbcatom1 = 0 pull_vec1 = 0.0 0.0 -1.0 pull_init1 = 0.058 -1.88226 -1.91169 pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000
