Re: [gmx-users] g_hbond : normalization autocorrelation function.
Erik,
I want autocorrelation function without normalization.
Exact value at t=0, t=1 is with normalization.
Nilesh
Hi Nilesh,
Iâm not sure what you mean. Both Ac_finSys and Ac are 1 at t=0. What
normalisation do you expect?
Kind regards,
Erik
Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College
Department of Chemistry
Physical Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ
On 19 Jul 2015, at 04:07, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote:
Hello,
I am calculating autocorrelation function without normalization using
g_hbond
g_hbond -f test.pdb -s 3.tpr -nonormalize -n hydrogen_1.ndx -ac
./test/hbac_3.xvg -num ./test/num_3.xvg
The output, hbac_3.xvg, don't have normalized auto correlation
function.
Here is initial part
@title Hydrogen Bond Autocorrelation
@xaxis label Time (ps)
@yaxis label C(t)
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend Ac\sfin sys\v{}\z{}(t)
@ s1 legend Ac(t)
@ s2 legend Cc\scontact,hb\v{}\z{}(t)
@ s3 legend -dAc\sfs\v{}\z{}/dt
0 1 1 6.67572e-060.761129
0.050.9619280.99214633980.401535
0.10.9598460.9917173496 0.0419408
0.150.9577340.9912813599 0.0340092
0.20.9564460.99101536600.022918
Why is it not normalized ?
Thanks,
Nilesh
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[gmx-users] g_hbond : normalization autocorrelation function.
Hello,
I am calculating autocorrelation function without normalization using g_hbond
g_hbond -f test.pdb -s 3.tpr -nonormalize -n hydrogen_1.ndx -ac
./test/hbac_3.xvg -num ./test/num_3.xvg
The output, hbac_3.xvg, don't have normalized auto correlation function.
Here is initial part
@title Hydrogen Bond Autocorrelation
@xaxis label Time (ps)
@yaxis label C(t)
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend Ac\sfin sys\v{}\z{}(t)
@ s1 legend Ac(t)
@ s2 legend Cc\scontact,hb\v{}\z{}(t)
@ s3 legend -dAc\sfs\v{}\z{}/dt
0 1 1 6.67572e-060.761129
0.050.9619280.99214633980.401535
0.10.9598460.9917173496 0.0419408
0.150.9577340.9912813599 0.0340092
0.20.9564460.99101536600.022918
Why is it not normalized ?
Thanks,
Nilesh
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Re: [gmx-users] g_hbond
Hello Erik, I did the same. Thanks, Nilesh Hi Nilesh, You could try gmx hbond -noda -r 0.25 -num hb.xvg, which should get the contacts in the last column of hb.xvg. Kind regards, Erik On 10 Jul 2015, at 15:58, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: I don't understand why am I not getting hydrogen bond,if I use cufoff 0.25nm? Nilesh But without contact you will need a full donor-hydrogen-acceptor triad for it to be registered, which is not what you want as far as I can tell. Erik On 10 Jul 2015, at 15:17, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: This is index file [ O8-H18-1 ] 8 18 [ O8-H18-2 ] 4032 Found 1 donors and 2 acceptors Its look contact YES check the distance between accetpr---donor. I will run without contact. Nilesh Hi Nilesh, Am not sure it accepts hydrogens as donors/acceptors even with -contact. How many donors and acceptors are found? Kind regards, Erik On 10 Jul 2015, at 14:37, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: I calculated number of hydrogen bond with cutoff 0.25 nm (Distance between hydrogen and O,acceptor) using g_hbond, g_hbond -f test.pdb -s 3.tpr -n hydrogen_1.ndx -num test_num.xvg -nonitacc -r 0.25 -contact -dist The found the calculated number of hydrogen bond along time are zero and -nan is the in hbdist.xvg file. I calculated the distance between hydrogen and oxygen using g_dist and the calculated the distance is less than 0.25 nm. Why am I getting zero number of hydrogen bonds using g_hbond (based on same cutoff )? Nilesh Thanks. I will use two groups. Nilesh On 7/9/15 9:13 PM, Nilesh Dhumal wrote: On 7/9/15 9:02 PM, Nilesh Dhumal wrote: Hello, I am calculating g_hbond for water system. I have a question about specifying two group for calculating hydrogen bond. Do I specify atoms in triplet(O-H---O)? Can I specify O-H as one group (Donor-Hydrogen) and O in other group (Acceptor)? If the system is pure water, you do not need any special index groups. I have DMSO in the system. I just mentioned water to make it simple. I am interested in O--H---O(DMSO) interactions? How should I specify this? With one triplet O--H---O(DMSO) or two groups one O--H and second O(DMSO) The latter - just use DMSO and water groups. O can be a donor or acceptor, and g_hbond intelligently figures out whether or not a given atom is a donor or acceptor (or both). -Justin Default -r cutoff is 0.35nm. Is the distance between hydrogen---acceptor or distance between donor---acceptor? Read the first sentence of the help description. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org
Re: [gmx-users] g_hbond
I don't understand why am I not getting hydrogen bond,if I use cufoff 0.25nm? Nilesh But without contact you will need a full donor-hydrogen-acceptor triad for it to be registered, which is not what you want as far as I can tell. Erik On 10 Jul 2015, at 15:17, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: This is index file [ O8-H18-1 ] 8 18 [ O8-H18-2 ] 4032 Found 1 donors and 2 acceptors Its look contact YES check the distance between accetpr---donor. I will run without contact. Nilesh Hi Nilesh, Am not sure it accepts hydrogens as donors/acceptors even with -contact. How many donors and acceptors are found? Kind regards, Erik On 10 Jul 2015, at 14:37, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: I calculated number of hydrogen bond with cutoff 0.25 nm (Distance between hydrogen and O,acceptor) using g_hbond, g_hbond -f test.pdb -s 3.tpr -n hydrogen_1.ndx -num test_num.xvg -nonitacc -r 0.25 -contact -dist The found the calculated number of hydrogen bond along time are zero and -nan is the in hbdist.xvg file. I calculated the distance between hydrogen and oxygen using g_dist and the calculated the distance is less than 0.25 nm. Why am I getting zero number of hydrogen bonds using g_hbond (based on same cutoff )? Nilesh Thanks. I will use two groups. Nilesh On 7/9/15 9:13 PM, Nilesh Dhumal wrote: On 7/9/15 9:02 PM, Nilesh Dhumal wrote: Hello, I am calculating g_hbond for water system. I have a question about specifying two group for calculating hydrogen bond. Do I specify atoms in triplet(O-H---O)? Can I specify O-H as one group (Donor-Hydrogen) and O in other group (Acceptor)? If the system is pure water, you do not need any special index groups. I have DMSO in the system. I just mentioned water to make it simple. I am interested in O--H---O(DMSO) interactions? How should I specify this? With one triplet O--H---O(DMSO) or two groups one O--H and second O(DMSO) The latter - just use DMSO and water groups. O can be a donor or acceptor, and g_hbond intelligently figures out whether or not a given atom is a donor or acceptor (or both). -Justin Default -r cutoff is 0.35nm. Is the distance between hydrogen---acceptor or distance between donor---acceptor? Read the first sentence of the help description. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se
Re: [gmx-users] g_hbond
I calculated number of hydrogen bond with cutoff 0.25 nm (Distance between hydrogen and O,acceptor) using g_hbond, g_hbond -f test.pdb -s 3.tpr -n hydrogen_1.ndx -num test_num.xvg -nonitacc -r 0.25 -contact -dist The found the calculated number of hydrogen bond along time are zero and -nan is the in hbdist.xvg file. I calculated the distance between hydrogen and oxygen using g_dist and the calculated the distance is less than 0.25 nm. Why am I getting zero number of hydrogen bonds using g_hbond (based on same cutoff )? Nilesh Thanks. I will use two groups. Nilesh On 7/9/15 9:13 PM, Nilesh Dhumal wrote: On 7/9/15 9:02 PM, Nilesh Dhumal wrote: Hello, I am calculating g_hbond for water system. I have a question about specifying two group for calculating hydrogen bond. Do I specify atoms in triplet(O-H---O)? Can I specify O-H as one group (Donor-Hydrogen) and O in other group (Acceptor)? If the system is pure water, you do not need any special index groups. I have DMSO in the system. I just mentioned water to make it simple. I am interested in O--H---O(DMSO) interactions? How should I specify this? With one triplet O--H---O(DMSO) or two groups one O--H and second O(DMSO) The latter - just use DMSO and water groups. O can be a donor or acceptor, and g_hbond intelligently figures out whether or not a given atom is a donor or acceptor (or both). -Justin Default -r cutoff is 0.35nm. Is the distance between hydrogen---acceptor or distance between donor---acceptor? Read the first sentence of the help description. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_hbond
This is index file [ O8-H18-1 ] 8 18 [ O8-H18-2 ] 4032 Found 1 donors and 2 acceptors Its look contact YES check the distance between accetpr---donor. I will run without contact. Nilesh Hi Nilesh, Am not sure it accepts hydrogens as donors/acceptors even with -contact. How many donors and acceptors are found? Kind regards, Erik On 10 Jul 2015, at 14:37, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: I calculated number of hydrogen bond with cutoff 0.25 nm (Distance between hydrogen and O,acceptor) using g_hbond, g_hbond -f test.pdb -s 3.tpr -n hydrogen_1.ndx -num test_num.xvg -nonitacc -r 0.25 -contact -dist The found the calculated number of hydrogen bond along time are zero and -nan is the in hbdist.xvg file. I calculated the distance between hydrogen and oxygen using g_dist and the calculated the distance is less than 0.25 nm. Why am I getting zero number of hydrogen bonds using g_hbond (based on same cutoff )? Nilesh Thanks. I will use two groups. Nilesh On 7/9/15 9:13 PM, Nilesh Dhumal wrote: On 7/9/15 9:02 PM, Nilesh Dhumal wrote: Hello, I am calculating g_hbond for water system. I have a question about specifying two group for calculating hydrogen bond. Do I specify atoms in triplet(O-H---O)? Can I specify O-H as one group (Donor-Hydrogen) and O in other group (Acceptor)? If the system is pure water, you do not need any special index groups. I have DMSO in the system. I just mentioned water to make it simple. I am interested in O--H---O(DMSO) interactions? How should I specify this? With one triplet O--H---O(DMSO) or two groups one O--H and second O(DMSO) The latter - just use DMSO and water groups. O can be a donor or acceptor, and g_hbond intelligently figures out whether or not a given atom is a donor or acceptor (or both). -Justin Default -r cutoff is 0.35nm. Is the distance between hydrogen---acceptor or distance between donor---acceptor? Read the first sentence of the help description. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://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
[gmx-users] g_hbond
Hello, I am calculating g_hbond for water system. I have a question about specifying two group for calculating hydrogen bond. Do I specify atoms in triplet(O-H---O)? Can I specify O-H as one group (Donor-Hydrogen) and O in other group (Acceptor)? Default -r cutoff is 0.35nm. Is the distance between hydrogen---acceptor or distance between donor---acceptor? Thanks, Nilesh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_hbond
Thanks. I will use two groups. Nilesh On 7/9/15 9:13 PM, Nilesh Dhumal wrote: On 7/9/15 9:02 PM, Nilesh Dhumal wrote: Hello, I am calculating g_hbond for water system. I have a question about specifying two group for calculating hydrogen bond. Do I specify atoms in triplet(O-H---O)? Can I specify O-H as one group (Donor-Hydrogen) and O in other group (Acceptor)? If the system is pure water, you do not need any special index groups. I have DMSO in the system. I just mentioned water to make it simple. I am interested in O--H---O(DMSO) interactions? How should I specify this? With one triplet O--H---O(DMSO) or two groups one O--H and second O(DMSO) The latter - just use DMSO and water groups. O can be a donor or acceptor, and g_hbond intelligently figures out whether or not a given atom is a donor or acceptor (or both). -Justin Default -r cutoff is 0.35nm. Is the distance between hydrogen---acceptor or distance between donor---acceptor? Read the first sentence of the help description. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_hbond
On 7/9/15 9:02 PM, Nilesh Dhumal wrote: Hello, I am calculating g_hbond for water system. I have a question about specifying two group for calculating hydrogen bond. Do I specify atoms in triplet(O-H---O)? Can I specify O-H as one group (Donor-Hydrogen) and O in other group (Acceptor)? If the system is pure water, you do not need any special index groups. I have DMSO in the system. I just mentioned water to make it simple. I am interested in O--H---O(DMSO) interactions? How should I specify this? With one triplet O--H---O(DMSO) or two groups one O--H and second O(DMSO) Default -r cutoff is 0.35nm. Is the distance between hydrogen---acceptor or distance between donor---acceptor? Read the first sentence of the help description. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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] HBlife time
Dear Gromacs Users, I am calculating hydrogen bond life time for water system. I have 128 water molecules in the system. The program scan the HB criteria for each OH bond with the rest 127 oxygen (128*128). For single OH bond I have calculated the HB lifetime. If there are more than 1 HB how does the program take care of all hydrogen bond for calculating HB lifetime? Does it calculate for each OH bond and take the average over the number of HBs? Thanks, Nilesh -- 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] qm-mm calculation : Gromacs + cpmd
Hello, I am planning to qm mm simulation with Gromacs + cpmd. Can I interface recent gromacs version (4.5.5) with cpmd (3.17.1)? Where can I find the information about interface? Thanks, Nilesh -- 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] Fatal error:No molecules were defined in the system
Hello, For grompp grompp -f minim_hy.mdp -c cu.gro -p test.top -o 1.tpr I get the error Fatal error:No molecules were defined in the system Here I pasted initial part of test.top file. ; Derived from parsing of runfiles/alat.top.orig [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_991 Cu2963.546001.098 A3.114e-010.02092e+00 opls_993 OA8 15.99940-0.665 A3.033e-01 0.401664e+00 opls_994 OB8 15.99940-0.665 A3.033e-01 0.401664e+00 opls_995 CA6 12.0110 0.778 A3.473e-01 0.39748e+00 opls_996 CB6 12.0110 -0.092 A3.473e-01 0.39748e+00 opls_997 CC6 12.0110 -0.014 A3.473e-01 0.39748e+00 opls_998 HM1 1.0080 0.109 A2.846e-01 0.06276e+00 [ moleculetype ] ; Namenrexcl BTC 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1opls_993 1BTCOA 1-0.66515.99940 2opls_995 1BTCCA 2 0.77812.01100 3opls_996 1BTCCB 3-0.09212.01100 4opls_997 1BTCCC 4-0.01412.01100 5opls_998 1BTCHM 5 0.109 1.00800 6opls_997 1BTCCC 6-0.01412.01100 7opls_998 1BTCHM 7 0.109 1.00800 8opls_993 1BTCOA 8-0.66515.99940 9opls_995 1BTCCA 9 0.77812.01100 10opls_996 1BTCCB 10-0.09212.01100 11opls_997 1BTCCC 11-0.01412.01100 12opls_998 1BTCHM 12 0.109 1.00800 13opls_993 1BTCOA 13-0.66515.99940 14opls_995 1BTCCA 14 0.77812.01100 15opls_996 1BTCCB 15-0.09212.01100 16opls_994 1BTCOB 16-0.66515.99940 17opls_994 1BTCOB 17-0.66515.99940 18opls_994 1BTCOB 18-0.66515.99940 19opls_993 1BTCOA 19-0.66515.99940 20opls_995 1BTCCA 20 0.77812.01100 Is there any error in .top file? Thanks, Nilesh -- 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] Fatal error:No molecules were defined in the system
I tried to send whole file. File is big. Can I forward to your personal email directly? Your mail to 'gromacs.org_gmx-users' with the subject Re: [gmx-users] Fatal error:No molecules were defined in the system Is being held until the list moderator can review it for approval. The reason it is being held: Message body is too big: 58940 bytes with a limit of 50 KB On 10/20/14 11:19 AM, Nilesh Dhumal wrote: Hello, For grompp grompp -f minim_hy.mdp -c cu.gro -p test.top -o 1.tpr I get the error Fatal error:No molecules were defined in the system Here I pasted initial part of test.top file. ; Derived from parsing of runfiles/alat.top.orig [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_991 Cu2963.546001.098 A3.114e-01 0.02092e+00 opls_993 OA8 15.99940-0.665 A3.033e-01 0.401664e+00 opls_994 OB8 15.99940-0.665 A3.033e-01 0.401664e+00 opls_995 CA6 12.0110 0.778 A3.473e-01 0.39748e+00 opls_996 CB6 12.0110 -0.092 A3.473e-01 0.39748e+00 opls_997 CC6 12.0110 -0.014 A3.473e-01 0.39748e+00 opls_998 HM1 1.0080 0.109 A2.846e-01 0.06276e+00 [ moleculetype ] ; Namenrexcl BTC 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1opls_993 1BTCOA 1-0.66515.99940 2opls_995 1BTCCA 2 0.77812.01100 3opls_996 1BTCCB 3-0.09212.01100 4opls_997 1BTCCC 4-0.01412.01100 5opls_998 1BTCHM 5 0.109 1.00800 6opls_997 1BTCCC 6-0.01412.01100 7opls_998 1BTCHM 7 0.109 1.00800 8opls_993 1BTCOA 8-0.66515.99940 9opls_995 1BTCCA 9 0.77812.01100 10opls_996 1BTCCB 10-0.09212.01100 11opls_997 1BTCCC 11-0.01412.01100 12opls_998 1BTCHM 12 0.109 1.00800 13opls_993 1BTCOA 13-0.66515.99940 14opls_995 1BTCCA 14 0.77812.01100 15opls_996 1BTCCB 15-0.09212.01100 16opls_994 1BTCOB 16-0.66515.99940 17opls_994 1BTCOB 17-0.66515.99940 18opls_994 1BTCOB 18-0.66515.99940 19opls_993 1BTCOA 19-0.66515.99940 20opls_995 1BTCCA 20 0.77812.01100 Is there any error in .top file? There is no way to tell unless you provide the full file. Either there is a syntax error somewhere that breaks the parsing, or your [molecules] section is empty. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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] pdb2gmx ffG43a1 force field
Hello, I am generating .top file using pdb2gmx and choose ffG43a1 force field from the list. pdb2gmx is running for an hour. Here I pasted the last part appeared on screen Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane dihedrals) 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 6: [DEPRECATED] Gromacs force field (see manual) 7: [DEPRECATED] Gromacs force field with hydrogens for NMR 8: Encad all-atom force field, using scaled-down vacuum charges 9: Encad all-atom force field, using full solvent charges 0 Opening library file /usr/share/gromacs/top/ffG43a1.rtp Opening library file /usr/share/gromacs/top/aminoacids.dat Opening library file /usr/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/share/gromacs/top/elements.dat Entries in elements.dat: 218 Reading cu.gro... Read 'Title', 156 atoms Opening library file /usr/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 156 atoms chain #res #atoms 1 '-' 1156 No occupancies in cu.gro Opening library file /usr/share/gromacs/top/ffG43a1.atp Atomtype 1 Cu Could any one tell why is it taking so long time. Total number of atom are 156 in system. Thanks, Nilesh -- 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] pdb2gmx ffG43a1 force field
All are from same residue. I added following part in .rtp file. [ BTC ] [ atoms ] Cu Cu 1.0980 OA O -0.665 0 OB O -0.665 0 CA C 0.778 0 CB C -0.092 0 CC C -0.014 0 HM H 0.109 0 [ bonds ] Cu OA gb_101 Cu OB gb_101 OA CA gb_102 OB CA gb_102 CA CB gb_103 CB CC gb_104 CC HM gb_105 [ angles ] OA Cu OA ga_101 OB Cu OB ga_101 OA Cu OB ga_102 Cu OA CA ga_103 Cu OB CA ga_103 OA CA OA ga_104 OB CA OB ga_104 OA CA OB ga_105 OA CA CB ga_106 OB CA CB ga_106 CA CB CC ga_107 CC CB CC ga_108 CB CC CB ga_109 CB CC HM ga_110 [ impropers ] ; aiajakal gromos type HMCC CB CB gd_103 CACB CC CC gd_104 CBCA OA OB gd_104 CBCA OB OA gd_104 [ dihedrals ] ; aiajakal gromos type CuOA CA CB gd_101 CuOB CA CB gd_101 CuOA CA OB gd_101 CuOB CA OA gd_101 CuOA CA OA gd_101 CuOB CA OB gd_101 CBCC CB CC gd_101 CACB CC CB gd_101 CACB CC HM gd_101 CCCB CC HM gd_101 OACA CB CC gd_102 OBCA CB CC gd_102 On 10/17/14 4:09 PM, Nilesh Dhumal wrote: Hello, I am generating .top file using pdb2gmx and choose ffG43a1 force field from the list. pdb2gmx is running for an hour. Here I pasted the last part appeared on screen Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane dihedrals) 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 6: [DEPRECATED] Gromacs force field (see manual) 7: [DEPRECATED] Gromacs force field with hydrogens for NMR 8: Encad all-atom force field, using scaled-down vacuum charges 9: Encad all-atom force field, using full solvent charges 0 Opening library file /usr/share/gromacs/top/ffG43a1.rtp Opening library file /usr/share/gromacs/top/aminoacids.dat Opening library file /usr/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/share/gromacs/top/elements.dat Entries in elements.dat: 218 Reading cu.gro... Read 'Title', 156 atoms Opening library file /usr/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 156 atoms chain #res #atoms 1 '-' 1156 No occupancies in cu.gro Opening library file /usr/share/gromacs/top/ffG43a1.atp Atomtype 1 Cu Could any one tell why is it taking so long time. Total number of atom are 156 in system. Please see my reply from earlier to this same post: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-October/092984.html -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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] .gro file units
Hello, I am converting .trr file to .gro file. trjconv -f structure_1.trr -s structure_1.tpr -pbc nojump -o structure_1.gro What are the unit of coordinate in .gro file? Is it angstrom? Thanks, Nilesh -- 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] pdb2gmx ffG43a1 force field
Hello, I am generating .top file using pdb2gmx and choose ffG43a1 force field from the list. pdb2gmx is running for an hour. Here I pasted the last part appeared on screen Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane dihedrals) 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 6: [DEPRECATED] Gromacs force field (see manual) 7: [DEPRECATED] Gromacs force field with hydrogens for NMR 8: Encad all-atom force field, using scaled-down vacuum charges 9: Encad all-atom force field, using full solvent charges 0 Opening library file /usr/share/gromacs/top/ffG43a1.rtp Opening library file /usr/share/gromacs/top/aminoacids.dat Opening library file /usr/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/share/gromacs/top/elements.dat Entries in elements.dat: 218 Reading cu.gro... Read 'Title', 156 atoms Opening library file /usr/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 156 atoms chain #res #atoms 1 '-' 1156 No occupancies in cu.gro Opening library file /usr/share/gromacs/top/ffG43a1.atp Atomtype 1 Cu Could any one tell why is it taking so long time. Total number of atom are 156 in system. Thanks, Nilesh -- 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] grompp Segmentation fault
hello, I running grompp for simulation. I get Segmentation fault error. grompp -f 600.mdp -c cu.gro -p cu_btc_1.top -o 1.tpr checking input for internal consistency... processing topology... Segmentation fault Could any one tell what is the problem? Thanks, Nilesh -- 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] Velocities from checkpoint
Hello, I am running 30ns simulation divided into 30 1ns simulations. I am saving the velocities each 5fs and I can't run a single 30ns simulation with saving velocities each 5 fs. I am running 30 simulations,each is 1ns. I get the velocities and delete the trajectory and go for next simulation. for (( i = 1; i = 29; i++)) do grompp -f md.mdp -c structure_1.pdb -p structure_1.top -o structure_1.tpr mdrun -s structure_1.tpr -o structure_1.trr -c structure_1.pdb -e structure_1.edr -g structure_1.log rm -f *#* trjconv -f structure_1.trr -s structure_1.tpr -pbc nojump -o structure_1.gro EOF 0 EOF ./dipole_rotational_translational_moment_append.out rm -f *#* rm structure_1.gro rm structure_1.trr done Each simulation Gromacs generate the velocities randomly which are independent on previous simulation. Could it possible to get the velocities based on previous simulation. Thanks, Nilesh -- 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] Reactive force field
Hello, Could it possible to run the simulation with reactive force field using Gromacs? Nilesh -- 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] Reactive force field
Hello, Could it possible to run the simulation with reactive force field using Gromacs? Nilesh -- 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] translational dipole moment during the simulation
Hello, I am calculating rotational and translational part of dipole moment. For translational dipole moment I want to save the velocities each 5fs and for rotational part I want to update trajectory each 2ps. I am running 30ns simulation. The size of trajectory is big and simulation get crashed because of less space. Could it possible to print only velocity at the center at each 5 fs? I am thinking to calculate the velocity at the center and the change during the simulation. How difficult to make this change in the code? Nilesh -- 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] berendsen vs parrinello-rahman
Hello, I am running the simulation for ionic liquids. I initially did simulation with Gromacs VERSION 4.0.7 with parrinello-rahman pressure coupling. Here I pasted temperature and pressure coupling part of mdp file. ; Temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc-grps =system ref_t = 350 ; Pressure coupling is on Pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 We updated gromacs version to recent Gromacs VERSION 4.5.5. With these parameter during equilibration, I got the error system is blowing up. I changed parrinello-rahman pressure coupling to berendsen and able to run the simulation. ; Temperature coupling is on ;Tcoupl = Nose-Hoover tau_t = 1.0 tc-grps =system ref_t = 400.0 ; Pressure coupling is on Pcoupl = berendsen; parrinello-rahman pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 Is there any changes in recent version in pressure coupling? Thanks Nilesh -- 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] berendsen vs parrinello-rahman
On 5/16/14, 11:37 AM, Nilesh Dhumal wrote: Hello, I am running the simulation for ionic liquids. I initially did simulation with Gromacs VERSION 4.0.7 with parrinello-rahman pressure coupling. Here I pasted temperature and pressure coupling part of mdp file. ; Temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc-grps =system ref_t = 350 ; Pressure coupling is on Pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 We updated gromacs version to recent Gromacs VERSION 4.5.5. With these parameter during equilibration, I got the error system is blowing up. I changed parrinello-rahman pressure coupling to berendsen and able to run the simulation. ; Temperature coupling is on ;Tcoupl = Nose-Hoover tau_t = 1.0 tc-grps =system ref_t = 400.0 ; Pressure coupling is on Pcoupl = berendsen; parrinello-rahman pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 Is there any changes in recent version in pressure coupling? Is there any prior equilibration? Using P-R for the initial phase of equilibration can be unstable. 4.0.7 was a bit more forgiving, and this same issue has been reported several times before with the 4.5.x series, with the solution being to set nstpcouple = 1 for the initial phase of equilibration with P-R. I did the simulations for two different initial structure. 1. Pre-equilibrated 2. New initial structure. Nilesh -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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] berendsen vs parrinello-rahman
One initial structure is equilibrated for 10ns using Gromacs VERSION 4.0.7. If I run same structure with same .mdp and same force field parameters using gromacs VERSION 4.5.5. I got the error system is blowing up. I made another new initial structure which is not equilibrated and I got the same error. After changing pressure coupling from parrinello-rahman to berendsen , both the simulations went well. Nilesh Unstable models or unstable initial conditions will behave unpredictably. Unfortunately you've not given us much to go on. Mark On May 16, 2014 6:08 PM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: On 5/16/14, 11:37 AM, Nilesh Dhumal wrote: Hello, I am running the simulation for ionic liquids. I initially did simulation with Gromacs VERSION 4.0.7 with parrinello-rahman pressure coupling. Here I pasted temperature and pressure coupling part of mdp file. ; Temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc-grps =system ref_t = 350 ; Pressure coupling is on Pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 We updated gromacs version to recent Gromacs VERSION 4.5.5. With these parameter during equilibration, I got the error system is blowing up. I changed parrinello-rahman pressure coupling to berendsen and able to run the simulation. ; Temperature coupling is on ;Tcoupl = Nose-Hoover tau_t = 1.0 tc-grps =system ref_t = 400.0 ; Pressure coupling is on Pcoupl = berendsen; parrinello-rahman pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 Is there any changes in recent version in pressure coupling? Is there any prior equilibration? Using P-R for the initial phase of equilibration can be unstable. 4.0.7 was a bit more forgiving, and this same issue has been reported several times before with the 4.5.x series, with the solution being to set nstpcouple = 1 for the initial phase of equilibration with P-R. I did the simulations for two different initial structure. 1. Pre-equilibrated 2. New initial structure. Nilesh -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] g_dipoles
Hello, I run g_dipoles for two different systems (System are ionic liquids). For one system when I run g_dipoles I get following message There are 256 molecules in the selection There are 256 charged molecules in the selection, will subtract their charge at their center of mass and I don't get this message for other system. Why program subtract their charge at their center of mass for one system and not for other. Nilesh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_dipoles
On 4/27/14, 4:25 PM, Nilesh Dhumal wrote: On 4/27/14, 4:01 PM, Nilesh Dhumal wrote: Hello, I run g_dipoles for two different systems (System are ionic liquids). For one system when I run g_dipoles I get following message There are 256 molecules in the selection There are 256 charged molecules in the selection, will subtract their charge at their center of mass and I don't get this message for other system. Why program subtract their charge at their center of mass for one system and not for other. Based on whatever the topology says, g_dipoles doesn't find a net charge on whatever these molecules are. Without providing more information - what the molecules/selections are, what the topology(ies) is(are) - that's all that can be surmised at this point. -Justin There are 128 cations (EMI) and 128 anions (ETS). Total charge is ZERO here is molecular section from topology file. [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 3 yes 0.5 0.5 #include emi.itp #include ets.itp [ molecules ] ; Compound#mols EMI128 ETS128 For other system I have different anion. I didn't specify the number of residues in molecular section. [ system ] ; Name Grunge ROck MAChoS t= 2.0 [ molecules ] ; Compound#mols Ion 1 Nilesh You said you had two different systems. What's the difference between them? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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] Dipole moment calculations
Hello, How does Gromacs calculate the dipole moment? Does it calculate the distance of a atom from origin (0.0,0.0,0.0) or distance from center of box (box_length/2, box_length/2, box_length/2) Nilesh -- 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] g_current
Hello, I am trying to calculate the correlation of the rotational and translational dipole moment of the system using g_current. There are 864 water molecules in the system. I run the following command, but its not writing the mc.xvg. g_current -f water.trr -s water.tpr -mc Could you tell whats going wrong? I am using Gromacs VERSION 4.5.5. Nilesh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_current
I checked with gmx_check, its says velocities found. Nilesh On 4/15/14, 11:50 AM, Nilesh Dhumal wrote: Hello, I am trying to calculate the correlation of the rotational and translational dipole moment of the system using g_current. There are 864 water molecules in the system. I run the following command, but its not writing the mc.xvg. g_current -f water.trr -s water.tpr -mc Could you tell whats going wrong? The only reason mc.xvg wouldn't be produced is if the input trajectory did not have velocities in it. Can you confirm with gmxcheck that your .trr has velocities? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_current
Here is full gmxcheck Checking file water.trr trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 # Atoms 2592 Last frame100 time 20.000 Item#frames Timestep (ps) Step 1010.2 Time 1010.2 Lambda 1010.2 Coords 1010.2 Velocities 0 Forces 0 Box1010.2 Checking coordinate file water.tpr Reading file water.tpr, VERSION 4.5.5 (single precision) Reading file water.tpr, VERSION 4.5.5 (single precision) 2592 atoms in file coordinates found box found velocities found Kinetic energy: 9695.08 (kJ/mol) Assuming the number of degrees of freedom to be Natoms * 3 or Natoms * 2, the velocities correspond to a temperature of the system of 299.908 K or 449.862 K respectively. Checking for atoms closer than 0.8 and not between 0.4 and 0.7, relative to sum of Van der Waals distance: WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. no close atoms found Atoms outside box ( 3.0273 3.0273 3.0273 ): (These may occur often and are normally not a problem) atom# name residue r_vdw coordinate 25 HW1 SOL 9 0.042.15 1.22 3.06 77 HW2 SOL 26 0.041.69 1.52 3.03 80 HW2 SOL 27 0.041.29 2.18 3.03 87 OW SOL 30 0.105 2.99 0.646 3.03 88 HW1 SOL 30 0.043.06 0.584 3.07 100 HW1 SOL 34 0.04 -0.0643 1.88 0.849 196 HW1 SOL 66 0.04 1.8 1.92 -0.0014 219 OW SOL 74 0.105 3.03 1.97 0.61 221 HW2 SOL 74 0.043.08 2.05 0.649 238 HW1 SOL 80 0.041.33 2.99 -0.0012 (maybe more) On 4/15/14, 2:18 PM, Nilesh Dhumal wrote: I checked with gmx_check, its says velocities found. Please provide the full gmxcheck output. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_current
Justin, Thanks for information. I run g_current for other system, ionic liquids. I checked the velocities using gmxcheck. I run, g_current -f 500.trr -s 500.tpr -mc There are two columns, I am not getting which rotational and translational. End of the file the function is infinity. Here I pasted the initial part of mc.xvg # This file was created Tue Apr 15 15:52:34 2014 # by the following command: # g_current -f 500.trr -s 500.tpr -mc # # g_current is part of G R O M A C S: # # Gravel Rubs Often Many Awfully Cauterized Sores # @title M\sD\N - current autocorrelation function @xaxis label Time (ps) @yaxis label M\sD\N (0)\c7\CJ(t) (e nm/ps)\S2 @TYPE xy # time M_D(0) J(t) acf Integral acf 0.000-0.140658 0 0.001-0.147092 -0.000386539 0.002-0.151369 -0.00119497 49.993-2.19596 51.7085 49.994-2.23022 51.6964 49.995-2.25746 51.6842 49.996-2.27946 51.6718 49.997-2.29797 51.6592 49.998 -2.3135 51.6466 49.999-2.32483 51.6339 50.000-inf 51.6211 Nilesh On 4/15/14, 2:27 PM, Nilesh Dhumal wrote: Here is full gmxcheck Checking file water.trr trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 # Atoms 2592 Last frame100 time 20.000 Item#frames Timestep (ps) Step 1010.2 Time 1010.2 Lambda 1010.2 Coords 1010.2 Velocities 0 There you have it; you didn't save velocities. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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.
