Re: [gmx-users] Restart -append
On 8/26/15 4:07 PM, Johnny Lu wrote: Dear Users, Simulation crashed. Gromacs 5.1 wrote last check point at about 4 min before the crash. Restart with mdrun -cpi (last check point file) -append Will the -append option get rid of the data for those 4 min between the last check point written and the crash? Yes, you can only resume from that time point that was saved in the .cpt file passed to -cpi. Anything that happened after that is overwritten. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] what's the easiest way to generate a md trajectory for ligand flying into/being pulled out of the pocket?
Thank you, Justin! Let me try. Cheers, Victor On Wed, Aug 26, 2015 at 10:57 AM, Justin Lemkul jalem...@vt.edu wrote: On 8/26/15 1:55 PM, Victor Ma wrote: Thanks James and Justin! My target is a big membrane protein. So far i've been using charmm-gui to set up my simulations. And for the movie, I need to keep the lipids. So with a charmm-gui pre-setup, can I still implement the pull code easily? The advice given does not depend on whether or not there are lipids. It's very simple to position the ligand in some straight line along which you pull it. -Justin Thanks!!! Victor On Wed, Aug 26, 2015 at 10:51 AM, Justin Lemkul jalem...@vt.edu wrote: On 8/26/15 1:47 PM, Barnett, James W wrote: Look into the pull code. You'll want to choose two groups (one for the ligand, one for the binding site), and one coordinate with those groups where the pull rate is not zero (negative rate to bring them together, positive rate to pull them apart). And if the purpose is just some cute movie that is not necessarily scientifically relevant (shakes head sadly), restrain the protein in some way to avoid the inherent problem of hitting a moving target. -Justin -- James “Wes” Barnett, Ph.D. Candidate Louisiana Board of Regents Fellow Chemical and Biomolecular Engineering Tulane University 341-B Lindy Boggs Center for Energy and Biotechnology 6823 St. Charles Ave New Orleans, Louisiana 70118-5674 jbarn...@tulane.edu From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Victor Ma victordsmag...@gmail.com Sent: Wednesday, August 26, 2015 12:31 PM To: gmx-us...@gromacs.org Subject: [gmx-users] what's the easiest way to generate a md trajectory for ligand flying into/being pulled out of the pocket? hello all I got a urgent request to make a MD movie for pulling the ligand out of the binding site/or the ligand flying into the pocket . I feel like i need to run something like steered md, which I've never done before. So can anyone please suggest a quick and dirty way to generate such a movie? Thank you!! Victor -- 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. -- == 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] Restart -append
Dear Users, Simulation crashed. Gromacs 5.1 wrote last check point at about 4 min before the crash. Restart with mdrun -cpi (last check point file) -append Will the -append option get rid of the data for those 4 min between the last check point written and the crash? Thank you. -- 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] what's the easiest way to generate a md trajectory for ligand flying into/being pulled out of the pocket?
On 8/26/15 1:47 PM, Barnett, James W wrote: Look into the pull code. You'll want to choose two groups (one for the ligand, one for the binding site), and one coordinate with those groups where the pull rate is not zero (negative rate to bring them together, positive rate to pull them apart). And if the purpose is just some cute movie that is not necessarily scientifically relevant (shakes head sadly), restrain the protein in some way to avoid the inherent problem of hitting a moving target. -Justin -- James “Wes” Barnett, Ph.D. Candidate Louisiana Board of Regents Fellow Chemical and Biomolecular Engineering Tulane University 341-B Lindy Boggs Center for Energy and Biotechnology 6823 St. Charles Ave New Orleans, Louisiana 70118-5674 jbarn...@tulane.edu From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Victor Ma victordsmag...@gmail.com Sent: Wednesday, August 26, 2015 12:31 PM To: gmx-us...@gromacs.org Subject: [gmx-users] what's the easiest way to generate a md trajectory for ligand flying into/being pulled out of the pocket? hello all I got a urgent request to make a MD movie for pulling the ligand out of the binding site/or the ligand flying into the pocket . I feel like i need to run something like steered md, which I've never done before. So can anyone please suggest a quick and dirty way to generate such a movie? Thank you!! Victor -- 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.
Re: [gmx-users] what's the easiest way to generate a md trajectory for ligand flying into/being pulled out of the pocket?
Thanks James and Justin! My target is a big membrane protein. So far i've been using charmm-gui to set up my simulations. And for the movie, I need to keep the lipids. So with a charmm-gui pre-setup, can I still implement the pull code easily? Thanks!!! Victor On Wed, Aug 26, 2015 at 10:51 AM, Justin Lemkul jalem...@vt.edu wrote: On 8/26/15 1:47 PM, Barnett, James W wrote: Look into the pull code. You'll want to choose two groups (one for the ligand, one for the binding site), and one coordinate with those groups where the pull rate is not zero (negative rate to bring them together, positive rate to pull them apart). And if the purpose is just some cute movie that is not necessarily scientifically relevant (shakes head sadly), restrain the protein in some way to avoid the inherent problem of hitting a moving target. -Justin -- James “Wes” Barnett, Ph.D. Candidate Louisiana Board of Regents Fellow Chemical and Biomolecular Engineering Tulane University 341-B Lindy Boggs Center for Energy and Biotechnology 6823 St. Charles Ave New Orleans, Louisiana 70118-5674 jbarn...@tulane.edu From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Victor Ma victordsmag...@gmail.com Sent: Wednesday, August 26, 2015 12:31 PM To: gmx-us...@gromacs.org Subject: [gmx-users] what's the easiest way to generate a md trajectory for ligand flying into/being pulled out of the pocket? hello all I got a urgent request to make a MD movie for pulling the ligand out of the binding site/or the ligand flying into the pocket . I feel like i need to run something like steered md, which I've never done before. So can anyone please suggest a quick and dirty way to generate such a movie? Thank you!! Victor -- 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] what's the easiest way to generate a md trajectory for ligand flying into/being pulled out of the pocket?
On 8/26/15 1:55 PM, Victor Ma wrote: Thanks James and Justin! My target is a big membrane protein. So far i've been using charmm-gui to set up my simulations. And for the movie, I need to keep the lipids. So with a charmm-gui pre-setup, can I still implement the pull code easily? The advice given does not depend on whether or not there are lipids. It's very simple to position the ligand in some straight line along which you pull it. -Justin Thanks!!! Victor On Wed, Aug 26, 2015 at 10:51 AM, Justin Lemkul jalem...@vt.edu wrote: On 8/26/15 1:47 PM, Barnett, James W wrote: Look into the pull code. You'll want to choose two groups (one for the ligand, one for the binding site), and one coordinate with those groups where the pull rate is not zero (negative rate to bring them together, positive rate to pull them apart). And if the purpose is just some cute movie that is not necessarily scientifically relevant (shakes head sadly), restrain the protein in some way to avoid the inherent problem of hitting a moving target. -Justin -- James “Wes” Barnett, Ph.D. Candidate Louisiana Board of Regents Fellow Chemical and Biomolecular Engineering Tulane University 341-B Lindy Boggs Center for Energy and Biotechnology 6823 St. Charles Ave New Orleans, Louisiana 70118-5674 jbarn...@tulane.edu From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Victor Ma victordsmag...@gmail.com Sent: Wednesday, August 26, 2015 12:31 PM To: gmx-us...@gromacs.org Subject: [gmx-users] what's the easiest way to generate a md trajectory for ligand flying into/being pulled out of the pocket? hello all I got a urgent request to make a MD movie for pulling the ligand out of the binding site/or the ligand flying into the pocket . I feel like i need to run something like steered md, which I've never done before. So can anyone please suggest a quick and dirty way to generate such a movie? Thank you!! Victor -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] what's the easiest way to generate a md trajectory for ligand flying into/being pulled out of the pocket?
Look into the pull code. You'll want to choose two groups (one for the ligand, one for the binding site), and one coordinate with those groups where the pull rate is not zero (negative rate to bring them together, positive rate to pull them apart). -- James “Wes” Barnett, Ph.D. Candidate Louisiana Board of Regents Fellow Chemical and Biomolecular Engineering Tulane University 341-B Lindy Boggs Center for Energy and Biotechnology 6823 St. Charles Ave New Orleans, Louisiana 70118-5674 jbarn...@tulane.edu From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Victor Ma victordsmag...@gmail.com Sent: Wednesday, August 26, 2015 12:31 PM To: gmx-us...@gromacs.org Subject: [gmx-users] what's the easiest way to generate a md trajectory for ligand flying into/being pulled out of the pocket? hello all I got a urgent request to make a MD movie for pulling the ligand out of the binding site/or the ligand flying into the pocket . I feel like i need to run something like steered md, which I've never done before. So can anyone please suggest a quick and dirty way to generate such a movie? Thank you!! Victor -- 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] Pull parameters to Restrain motion along the Z Axis
Hi, I use Gromacs 4.5.5. I have these pull parameters which I use to restrain my Protein motion along the Z axis.I want to make sure these parameters are fine or not since , I am not getting expected results. Also, please suggest any other parameters I can add. ;Pull to restrain Z position pull = umbrella pull_geometry= distance ; Select components for the pull vector. default: Y Y Y pull_dim = N N Y pull_start = No pull_nstxout = 1 pull_nstfout = 1 pull_ngroups = 1 pull_group0 = DPPC pull_group1 = Protein pull_vec1= 0.0 0.0 0.0 pull_init1 = 1.0 pull_rate1 = 0 pull_k1 = 1000 pull_kB1 = 1000 Here I am completely confused in pull_init and pull_start. From my understanding, pull_init is the reference distance at t=0. The reference distance is the distance between COM of the pull group and COM of the reference group.I have set my reference group as DPPC and pull group as Protein, which means my Z_distance should be Ideally ~ 1.00 if my pull_start is set up as No and should be ~0.0 if that is set it as Yes.Since, pull_start means the initial COM distance is the reference distance for the first frame. But my values are instead after the production run:- with pull_init =1.0 and pull_start = Yes time |d| dx dy dz 0.0004.53616050.98503492.36917383.7407854 with pull_init =1.0 and pull_start= No 0.0002.82224150.78675102.5469491 -0.9268878 my protein is nearly at the center of membrane of box size 7.34147 7.34147 7.34147 If somebody can help me I will be grateful. Thanks, Vikas -- 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] implicit solvation on gpu
hi i want to perform implicit solvent simulation of a prion protein on gpu. the cutoff-scheme I used is Verlet, but it gives error Implicit solvent is not (yet) supported with the with Verlet lists.i cannot use cutoff-scheme= group because it is not suitable for gpu. also i have set the verlet lists to zero/infinity but giving errors. please guide me. 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] probability distributions in gmx
On 8/26/15 1:20 AM, RJ wrote: Dear gmx, I understand that probability distributions of distance can be calculated through gmx analyze tool but how the probability distributions of others such as SASA and secondary structure can be calculated? Correction: gmx analyze can be used to create distributions of *any* time series in an .xvg file. It's not limited to just distance. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Helicity over simulation time?
On 8/25/15 10:20 PM, Rajiv wrote: Dear all, I have performed 200ns simulation for a protein and wants to plot a helicity over simulation time. After reading few queries, i have done do_dssp and obtained the scount.xvg which has the all secondary structure as a function time. I wonder, how do i only obtain the helicity over function of time as i want to plot the probability distribution of helicity. You basically have this information - scount.xvg has the number of helical residues in each frame. Divide by the total number of residues and you have the fraction of helix over time. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] calculate average and maximum non-bonded energy between energy groups
On 8/26/15 5:55 AM, Tushar Ranjan Moharana wrote: Hi Vitaly, Thanks for your suggestion. I have 30 energy groups. I faced following problems while using gmx energy. 1) With gmx energy there are more than 3000 options to choose from. All the options are not visible in terminal because of large number. There for I cann't proceed further. Use a bigger terminal, or at least one that allows scrolling... 2) Output of gmx energy is a .xvg file with X axis as time and Y axis as energy between 2 groups. To get the data the way I need (X axis energy group and Y axis total energy with all other groups) I have to again process them with some other tool. Right, see gmx analyze. Out put of gmx energy has time in X axis and energy in Y axis. The maximum value of which I referred to as maximum interaction energy. (This mayn't be the exact definition). I would agree with Vitaly that this is really not a useful quantity. It is force field-specific and not necessarily anything to do with thermodynamics or free energy. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pairwise h-bonds
Hi, Note however that each line is a specific donor-acceptor pair. All the information you need is in that matrix and the corresponding index file. 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 24 Aug 2015, at 09:46, bernhard morpheus.sommer2...@gmail.com wrote: Sorry I had a typo in my previous email: I have used the -hbm and -hbn option (not the -m as it does not exist). The problem is however that this option gives me the h-bonds for each residues of group 1 to _any_ residue of group 2 and not the pairwise h-bonds between all members of group 1 and group 2. i.e. it gives a 100x1000 matrix instead of a 100x100x1000 matrix. I guess I am not the first person enountering this problem so there must be a quite simple solution got get all pairwise h-bonds but I can't figure it out ... Best, Morpheus Erik Marklund erik.marklund at chem.ox.ac.uk Sat Aug 22 22:03:26 CEST 2015 Previous message: [gmx-users] pairwise h-bonds Dear Morpheus, Try the -hbn and -hbm options. The latter generates a similar matrix and the former is essentially a dictionary to that matrix. Kind regards, Erik On 21 Aug 2015, at 12:45, bernhard morpheus.sommer2008 at gmail.com wrote: Dear Gromacs users, I was wondering about the best way of obtaining pairwise h-bonds of certain residues. I got about 100 residues of interest and 1000 simulation frames. I would like to get the h-bonds at each timeframe between each pair of residues. i.e. a matrix with 100x100x1000. At the moment I have created an index group for each residue and run the pairwise h-bond calculations in two nested loops via a perl script. The problem is that this takes long and also creates 10 000 000 files on the harddisk which I then need to parse with another skript. Is there an easier way? I have also tried to use the -m option with protein and protein as input groups but this also those not give the pairwise h-bonds but rather the cumulative ones per residue against all 100 residues. Can anyone give me a hint? Cheers, Morpheus -- 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] force-force correlation function
Hi all, Is there way to estimate the force-force correlation function in gromacs? bests -- 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] Coulomb barriers and Coulomb Softcore Potential
Dear Mr. Shirts, thanks for your reply. My N/N_k ratio looks like this: Number of correlated and uncorrelated samples: StateN N_kN/N_k 0 613148319.06 1 613112219.28 2 613496117.16 3 61 937464.01 4 61 2249 266.86 5 61 532 1129.04 6 61 94 6384.18 7 61 485 1237.84 8 61 585 1027.03 9 61 1684 356.43 10 61 1047 573.48 11 61 820773.11 12 61 347 1731.24 13 61 2702 222.13 14 61 79 7692.14 15 61 193 3120.28 16 61 414 1451.40 17 615798510.35 18 6160589 9.90 19 6164621 9.28 With the following lambda distribution: ; init_lambda_state0 1 2 3 4 5 6 7 8 9 1011121314151617 18 19 vdw_lambdas = 0.000 0.224 0.378 0.489 0.578 0.657 0.730 0.802 0.881 0.976 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 coul_lambdas= 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.100 0.210 0.303 0.383 0.452 0.524 0.604 0.712 0.853 1.000 and lambda values 0 = decoupled / 1 = coupled. I use the LJ 1-1-6 SCP with alpha = 0.7 (I've checked alpha = 0.5 as well, but there is no significant difference), while Coulomb Softcore is not active. I've uploaded a diagram of Gibbs free energy difference over simulation time on github (https://github.com/AMecklenfeld/Ionic-Liquid/issues/1). The diagram contains some plateaus with high steps and slowly approaches a final value. From my point of view, it actually looks like my system is this slow. My idea was to use the Coulomb-SCP to flatten the energetic landscape. Another way would be expanded ensemble simulation, but since I use a constrained 4-site water model (triangle constraints), I've difficulties with shake in Gromacs 5.0.4. Do you have any suggestions? With kind regards, Andreas Mecklenfeld Am 24.08.2015 um 17:08 schrieb Michael Shirts: Adjusting the soft core is a gigantic pain. I wouldn't recommend it, and it's likely not necesssary. What settings are you using now? Note that the manual describes how it is defined. Can you post the alchemical-analysis output for N/N_k? There's an analysis quirk we are looking at where the correlation times are measured to be longer than they actually are, though that is when LJ is changing and coul is turned off. Look at the time correlation for the variable that is changing -- does it look stationary, or does it look like it's changing slowly, or has just a few discrete steps? If the autocorrelation time is slow, then N/N_k actually is that long, and the code is doing it's job. On Mon, Aug 24, 2015 at 9:55 AM, Andreas Mecklenfeld a.mecklenf...@tu-braunschweig.de wrote: Dear Gromacs-Users, I want to calculate the solvation free energy of water in an aqueous ionic solution and I'm using the Python tool alchemical-analysis.py by Klimovich, Shirts and Mobley for evaluation. This tool demonstrates a very high N/N_k ratio (up to 7000) while decreasing the electrostatic potential (Lennard Jones fully active). Considering energetic barriers, I would like to adjust the Coulomb Softcore Potential. Does this seem plausible and if so, how is the Coulomb Softcore Potential defined in Gromacs? Naden and Shirts provide a concept by equation (A.2) in Linear Basis Function Approach to Efficient Alchemical Free Energy Calculations. 2. Inserting and Deleting Particles with Coulombic Interactions (http://pubs.acs.org/doi/abs/10.1021/ct501047e) - is this the formula intended? Best regards, Andreas -- M. Sc. Andreas Mecklenfeld Stipendiat Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 Fax: +49 (0)531 391-7814 www.ift-bs.de -- 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. -- M. Sc. Andreas Mecklenfeld Stipendiat Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 Fax: +49 (0)531 391-7814 http://www.ift-bs.de -- Gromacs Users mailing list * Please search the archive at
Re: [gmx-users] Input files for performance analysis
Hi, On 25 Aug 2015, at 20:23, Sabyasachi Sahoo ssahoo.i...@gmail.com wrote: Hello all, I have good enough experience in high performance and parallel computing and would like to find out bottlenecks in various phases of GROMACS. Can anyone please give me links to ready-to run input files of standard molecular systems to be simulated for GROMACS (to be run on supercomputers with hundreds to thousands of cores) so that I can skip the detailed learning of writing individual parameters and focus on results obtained from profilers( both internal and external profilers for GROMACS. Related study material or latest papers showing such analysis will also prove to be immensely helpful. I can advertise these recent GROMACS papers: http://dx.doi.org/10.1002/jcc.24030 http://dx.doi.org/10.1007/978-3-319-15976-8_1 http://pubman.mpdl.mpg.de/pubman/item/escidoc:2037317/component/escidoc:2037318/2037317.pdf?mode=download Carsten Thanks in advance! -- Yours sincerely, Saby -- 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] calculate average and maximum non-bonded energy between energy groups
Hi Vitaly, Thanks for your suggestion. I have 30 energy groups. I faced following problems while using gmx energy. 1) With gmx energy there are more than 3000 options to choose from. All the options are not visible in terminal because of large number. There for I cann't proceed further. 2) Output of gmx energy is a .xvg file with X axis as time and Y axis as energy between 2 groups. To get the data the way I need (X axis energy group and Y axis total energy with all other groups) I have to again process them with some other tool. Out put of gmx energy has time in X axis and energy in Y axis. The maximum value of which I referred to as maximum interaction energy. (This mayn't be the exact definition). Please let me know if you have any solution for the above problem. If anybody else also know the solution please share with me. Thanks a lot in advance. A society with free knowledge is better than a society with free food Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- 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] Pull parameters to Restrain motion along the Z Axis
pull_start = yes means COM distance is added to the pull_init value. So whatever distance your two pull groups starts out at plus pull_init is the window where it will sample. pull_start = no means just the pull_init value is used as the reference distance. If you have pull_init set to 1.0 then that is the reference distance for sampling (the window where it will sample). If you haven't equilibrated at the reference distance it could take a little bit for your two groups to get to the reference distance. At t=0 nothing has moved yet, unless you have equilibrated with the same pull code parameters already (and you probably should, depending on what your goal is here), so you should not expect the distance between the two groups to already be near the reference distance before the simulation has begun. If you're looking to restrain the protein's movement to the z-axis such that it can only move along the z-axis, this is not what you'll be achieving. Here are you restricting the movement of the protein along the z-axis but it is free to move in the x and y directions. I may be misunderstanding your goal here. There are some flat-bottom restraints you can add to make it such that the protein only moves in one direction if that's your goal. Check the relevant sections in the manual. -- James “Wes” Barnett, Ph.D. Candidate Louisiana Board of Regents Fellow Chemical and Biomolecular Engineering Tulane University 341-B Lindy Boggs Center for Energy and Biotechnology 6823 St. Charles Ave New Orleans, Louisiana 70118-5674 jbarn...@tulane.edu From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Live King vikasdubey1...@gmail.com Sent: Wednesday, August 26, 2015 5:25 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Pull parameters to Restrain motion along the Z Axis Hi, I use Gromacs 4.5.5. I have these pull parameters which I use to restrain my Protein motion along the Z axis.I want to make sure these parameters are fine or not since , I am not getting expected results. Also, please suggest any other parameters I can add. ;Pull to restrain Z position pull = umbrella pull_geometry= distance ; Select components for the pull vector. default: Y Y Y pull_dim = N N Y pull_start = No pull_nstxout = 1 pull_nstfout = 1 pull_ngroups = 1 pull_group0 = DPPC pull_group1 = Protein pull_vec1= 0.0 0.0 0.0 pull_init1 = 1.0 pull_rate1 = 0 pull_k1 = 1000 pull_kB1 = 1000 Here I am completely confused in pull_init and pull_start. From my understanding, pull_init is the reference distance at t=0. The reference distance is the distance between COM of the pull group and COM of the reference group.I have set my reference group as DPPC and pull group as Protein, which means my Z_distance should be Ideally ~ 1.00 if my pull_start is set up as No and should be ~0.0 if that is set it as Yes.Since, pull_start means the initial COM distance is the reference distance for the first frame. But my values are instead after the production run:- with pull_init =1.0 and pull_start = Yes time |d| dx dy dz 0.0004.53616050.98503492.36917383.7407854 with pull_init =1.0 and pull_start= No 0.0002.82224150.78675102.5469491 -0.9268878 my protein is nearly at the center of membrane of box size 7.34147 7.34147 7.34147 If somebody can help me I will be grateful. Thanks, Vikas -- 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] Position restrain Bilayer
Hey folks!
I want to position restrain my lipid bilayer for minimization and equibriliation, but grommp gives me following error:
Fatal error:
[ file posresdppe.itp, line 17 ]:
Atom index (13) in position_restraints out of bounds (1-12).
I generated the *.itp files with genrestr -f membrane-ecoli.gro -n index.ndx -o posres{insert lipidname}.itp, making sure atom indices match with my index file.
I think Ive put them in the right order in the topology:
#include martini.itp
#include martini_ions.itp
[ moleculetype ]
#include DPPE.itp
#ifdef POSRES_LIPID
#include posresdppe.itp
#endif
#include DOPE.itp
#ifdef POSRES_LIPID
#include posresdope.itp
#endif
#include POPE.itp
#ifdef POSRES_LIPID
#include posrespope.itp
#endif
#include POPG.itp
#ifdef POSRES_LIPID
#include posrespopg.itp
#endif
[ system ]
e coli membrane
[ molecules ]
DPPE 61
DOPE 61
POPE 61
POPG 61
DPPE 61
DOPE 61
POPE 61
POPG 61
W 7166
NA+ 140
CL- 18
So whats wrong? Do you have an idea?
Thanks in advance! :)
Warm regards,
Kathrin
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Re: [gmx-users] Position restrain Bilayer
On 8/26/15 10:57 AM, kh...@web.de wrote:
Hey folks!
I want to position restrain my lipid bilayer for minimization and
equibriliation, but grommp gives me following error:
Fatal error:
[ file posresdppe.itp, line 17 ]:
Atom index (13) in position_restraints out of bounds (1-12).
I generated the *.itp files with genrestr -f membrane-ecoli.gro -n index.ndx -o
posres{insert lipidname}.itp, making sure atom indices match with my index file.
genrestr can only work with a single molecule. Note the caveat in the help
description. If you're feeding it something with multiple molecules, it won't
work (OK, there are ways around that or that you can fix it afterwards, but keep
it simple).
-Justin
I think I've put them in the right order in the topology:
#include martini.itp
#include martini_ions.itp
[ moleculetype ]
#include DPPE.itp
#ifdef POSRES_LIPID
#include posresdppe.itp
#endif
#include DOPE.itp
#ifdef POSRES_LIPID
#include posresdope.itp
#endif
#include POPE.itp
#ifdef POSRES_LIPID
#include posrespope.itp
#endif
#include POPG.itp
#ifdef POSRES_LIPID
#include posrespopg.itp
#endif
[ system ]
e coli membrane
[ molecules ]
DPPE61
DOPE61
POPE61
POPG61
DPPE61
DOPE61
POPE61
POPG61
W 7166
NA+140
CL- 18
So whats wrong? Do you have an idea?
Thanks in advance! :)
Warm regards,
Kathrin
--
==
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
==
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Re: [gmx-users] calculate average and maximum non-bonded energy between energy groups
Hi Justin, Thanks for your precious advice. You replied that I would agree with Vitaly that this is really not a useful quantity. It is force field-specific and not necessarily anything to do with thermodynamics or free energy. did you refer to maximum energy or average energy or both. You also adviced to use a terminal that allows scrolling. Now I am able to scroll in my terminal. However I read in many places about gmx enemat which can extract energy matrix. How ever in my case it gives following error. Read 40 groups group 0WARNING! could not find group Coul-SR:VAL171-VAL171 (0,0)in energy file WARNING! could not find group LJ-SR:VAL171-VAL171 (0,0)in energy file WARNING! could not find group Coul-SR:VAL171-MET173 (0,1)in energy file WARNING! could not find group LJ-SR:VAL171-MET173 (0,1)in energy file WARNING! could not find group Coul-SR:VAL171-VAL174 (0,2)in energy file WARNING! could not find group LJ-SR:VAL171-VAL174 (0,2)in energy file WARNING! could not find group Coul-SR:VAL171-VAL187 (0,3)in energy file WARNING! could not find group LJ-SR:VAL171-VAL187 (0,3)in energy file WARNING! could not find group Coul-SR:VAL171-ILE203 (0,4)in energy file WARNING! could not find group LJ-SR:VAL171-ILE203 (0,4)in energy file WARNING! could not find group Coul-SR:VAL171-TYR204 (0,5)in energy file ... group 38WARNING! could not find group Coul-SR:ODE-ODE (38,38)in energy file WARNING! could not find group LJ-SR:ODE-ODE (38,38)in energy file WARNING! could not find group Coul-SR:ODE-ODA (38,39)in energy file WARNING! could not find group LJ-SR:ODE-ODA (38,39)in energy file group 39 Will select half-matrix of energies with 2 elements Last energy frame read 2000 time 2000.000 Will build energy half-matrix of 40 groups, 2 elements, over 2001 frames Segmentation fault (core dumped) I read from GROMACS user mailing list where you have suggested someone to install GROMACS in debug mode or use GROMACS-4.6.5. I have tried both but nothing worked for me. am I doing any mistake? My energygrp-excl is empty as it is not supported by Verlet. In the above case what ever group was not found by gmx enemat was read by gmx energy and gives output in the same .edr file. Thank you in advance. A society with free knowledge is better than a society with free food Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- 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 do I calculate the difference between two energy values?
Let x(t) be coulomb decoupling at time t. Let y(t) be VdW decoupling at time t. I guess the most safe way to get the answer is: calculate z(t) = x(t) + y(t) then, calculate standard deviation of z(t). If x(t) and y(t) are independent and both x(t) and y(t) are normally distributed, then I guess using the error propagation rule is fine. (https://en.wikipedia.org/wiki/Sum_of_normally_distributed_random_variables) On Tue, Aug 25, 2015 at 2:15 PM, Peter Stern peter.st...@weizmann.ac.il wrote: I believe that this is a statistics question and not a gromacs question :-). 51.4 +/- 1.33 kJ/mol Sent from my iPad On 25 באוג׳ 2015, at 14:44, minky son minky0...@gmail.com wrote: Dear GROMACS users, I have been studying free energy calculation in Justin tutorial. I performed VDW decoupling and coulomb decoupling simulations separately. I obtained the free energy values for each simulation using gmx bar. coulomb decoupling simulation = 60.88 +/- 0.23 kJ/mol VDW decoupling simulation= -9.48 +/- 1.31 kJ/mol So, I want to calculate the sum of the two energy values, specially the second term (51.4 +/- ???). Please give me any advice to solve this. Regards, -- 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] sanjay (membrane dynamics)
HI, I am running memebrane dynamics. I have prepared all the supportive files.At command prompt i am getting an error Source code file: topio.c, line: 656 Fatal error:Syntax error - File topol.top, line 7155Last line read:'[ system ]'Invalid order for directive system I am unable to interprete what does it mean? Please help me. Thanking you -- 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] autocorrelation function
Dear sir , How can we compute the autocorrelation function of the temperature or kinetic energy ? I want to calculate thermal conductivity of noble gases from green - kubo formalism. -- 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 fix a molecule's initial configuration
Some one suggest position restraint at https://www.mail-archive.com/gmx-users@gromacs.org/msg21569.html , Can that restraint allow the restrainted molecule freely translate or rotate with a fixed configuration? Thank you. yours xiaodong Research School of Chemistry ANU 2015-08-27 11:56 GMT+08:00 li he parachuternewy...@gmail.com: Dear gmxers, I want to fix a molecule's, e.g. octanol's, initial configuration in Gromacs MD simulation. I find some hints at https://www.mail-archive.com/gmx-users@gromacs.org/msg21569.html It reads that, I can apply distance restraint or use RMSD umbrella sampling with PLUMED. I wonder if there is smarter way to do that with GROMACS, since 6 years has past since that post? e.g. Does Gromacs has some utility similar to CHARMM's RMSD restraint (CONS RMSD at http://www.charmm.org/documentation/c33b2/cons.html# RMSD restraints)? Any suggestion or comment will be highly appreciated. Thank you. yours xiaodong Research School of Chemistry ANU -- 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 fix a molecule's initial configuration
Dear gmxers, I want to fix a molecule's, e.g. octanol's, initial configuration in Gromacs MD simulation. I find some hints at https://www.mail-archive.com/gmx-users@gromacs.org/msg21569.html It reads that, I can apply distance restraint or use RMSD umbrella sampling with PLUMED. I wonder if there is smarter way to do that with GROMACS, since 6 years has past since that post? e.g. Does Gromacs has some utility similar to CHARMM's RMSD restraint (CONS RMSD at http://www.charmm.org/documentation/c33b2/cons.html# RMSD restraints)? Any suggestion or comment will be highly appreciated. Thank you. yours xiaodong Research School of Chemistry ANU -- 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.
