Re: [gmx-users] Fwd: Lysosyme in water
source .../gromacs.5.x/build/bin/GMXRC Ommair On Mon, Jun 5, 2017 at 12:45 AM, shivanigupta.gup...@gmail.com < shivanigupta.gup...@gmail.com> wrote: > Dear Gromacs > > I am new and a beginner to this system. I am trying to learn through > tutorials for version 5. When i performed i got the following error . > [shivani@POLY3 tut1]$ editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c > -d 1.0 -bt cubic > -bash: editconf: command not found > [shivani@POLY3 tut1]$ gmx editconf -f 1AKI_processed.gro -o > 1AKI_newbox.gro > -c -d 1.0 -bt cubic > -bash: gmx: command not found > [shivani@POLY3 tut1]$ gmx_mpi editconf -f 1AKI_processed.gro -o > 1AKI_newbox.gro -c -d 1.0 -bt cubic > -bash: gmx_mpi: command not found > [shivani@POLY3 tut1]$ gmpp editconf -f 1AKI_processed.gro -o > 1AKI_newbox.gro -c -d 1.0 -bt cubic > -bash: gmpp: command not found > [shivani@POLY3 tut1]$ ls > 1AKI.pdb 1AKI_processed.gro posre.itp topol.top > [shivani@POLY3 tut1]$ ll > total 812 > -rw-rw-r-- 1 shivani shivani 116316 Jun 1 15:24 1AKI.pdb > -rw-rw-r-- 1 shivani shivani 98776 Jun 1 15:10 1AKI_processed.gro > -rw-rw-r-- 1 shivani shivani 31304 Jun 1 15:10 posre.itp > -rw-rw-r-- 1 shivani shivani 576928 Jun 1 15:10 topol.top > [shivani@POLY3 tut1]$ > > Can you help me in fixing the same . > > Thanks > Regards > Shivani > -- > 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] Fwd: Lysosyme in water
And don't forget to source first then use commands described in previous email as follows, Source GMXRC On Jun 5, 2017 12:46 AM, "shivanigupta.gup...@gmail.com" < shivanigupta.gup...@gmail.com> wrote: > Dear Gromacs > > I am new and a beginner to this system. I am trying to learn through > tutorials for version 5. When i performed i got the following error . > [shivani@POLY3 tut1]$ editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c > -d 1.0 -bt cubic > -bash: editconf: command not found > [shivani@POLY3 tut1]$ gmx editconf -f 1AKI_processed.gro -o > 1AKI_newbox.gro > -c -d 1.0 -bt cubic > -bash: gmx: command not found > [shivani@POLY3 tut1]$ gmx_mpi editconf -f 1AKI_processed.gro -o > 1AKI_newbox.gro -c -d 1.0 -bt cubic > -bash: gmx_mpi: command not found > [shivani@POLY3 tut1]$ gmpp editconf -f 1AKI_processed.gro -o > 1AKI_newbox.gro -c -d 1.0 -bt cubic > -bash: gmpp: command not found > [shivani@POLY3 tut1]$ ls > 1AKI.pdb 1AKI_processed.gro posre.itp topol.top > [shivani@POLY3 tut1]$ ll > total 812 > -rw-rw-r-- 1 shivani shivani 116316 Jun 1 15:24 1AKI.pdb > -rw-rw-r-- 1 shivani shivani 98776 Jun 1 15:10 1AKI_processed.gro > -rw-rw-r-- 1 shivani shivani 31304 Jun 1 15:10 posre.itp > -rw-rw-r-- 1 shivani shivani 576928 Jun 1 15:10 topol.top > [shivani@POLY3 tut1]$ > > Can you help me in fixing the same . > > Thanks > Regards > Shivani > -- > 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] Fwd: Lysosyme in water
Start your command as follows then write whatever you to do gmx_mpi editconf .. On Jun 5, 2017 12:46 AM, "shivanigupta.gup...@gmail.com" < shivanigupta.gup...@gmail.com> wrote: > Dear Gromacs > > I am new and a beginner to this system. I am trying to learn through > tutorials for version 5. When i performed i got the following error . > [shivani@POLY3 tut1]$ editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c > -d 1.0 -bt cubic > -bash: editconf: command not found > [shivani@POLY3 tut1]$ gmx editconf -f 1AKI_processed.gro -o > 1AKI_newbox.gro > -c -d 1.0 -bt cubic > -bash: gmx: command not found > [shivani@POLY3 tut1]$ gmx_mpi editconf -f 1AKI_processed.gro -o > 1AKI_newbox.gro -c -d 1.0 -bt cubic > -bash: gmx_mpi: command not found > [shivani@POLY3 tut1]$ gmpp editconf -f 1AKI_processed.gro -o > 1AKI_newbox.gro -c -d 1.0 -bt cubic > -bash: gmpp: command not found > [shivani@POLY3 tut1]$ ls > 1AKI.pdb 1AKI_processed.gro posre.itp topol.top > [shivani@POLY3 tut1]$ ll > total 812 > -rw-rw-r-- 1 shivani shivani 116316 Jun 1 15:24 1AKI.pdb > -rw-rw-r-- 1 shivani shivani 98776 Jun 1 15:10 1AKI_processed.gro > -rw-rw-r-- 1 shivani shivani 31304 Jun 1 15:10 posre.itp > -rw-rw-r-- 1 shivani shivani 576928 Jun 1 15:10 topol.top > [shivani@POLY3 tut1]$ > > Can you help me in fixing the same . > > Thanks > Regards > Shivani > -- > 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] Fwd: Lysosyme in water
gmx editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 1.0 -bt cubic Try the above command On Mon, 5 Jun 2017 at 10:16 AM, shivanigupta.gup...@gmail.com < shivanigupta.gup...@gmail.com> wrote: > Dear Gromacs > > I am new and a beginner to this system. I am trying to learn through > tutorials for version 5. When i performed i got the following error . > [shivani@POLY3 tut1]$ > -bash: editconf: command not found > [shivani@POLY3 tut1]$ gmx editconf -f 1AKI_processed.gro -o > 1AKI_newbox.gro > -c -d 1.0 -bt cubic > -bash: gmx: command not found > [shivani@POLY3 tut1]$ gmx_mpi editconf -f 1AKI_processed.gro -o > 1AKI_newbox.gro -c -d 1.0 -bt cubic > -bash: gmx_mpi: command not found > [shivani@POLY3 tut1]$ gmpp editconf -f 1AKI_processed.gro -o > 1AKI_newbox.gro -c -d 1.0 -bt cubic > -bash: gmpp: command not found > [shivani@POLY3 tut1]$ ls > 1AKI.pdb 1AKI_processed.gro posre.itp topol.top > [shivani@POLY3 tut1]$ ll > total 812 > -rw-rw-r-- 1 shivani shivani 116316 Jun 1 15:24 1AKI.pdb > -rw-rw-r-- 1 shivani shivani 98776 Jun 1 15:10 1AKI_processed.gro > -rw-rw-r-- 1 shivani shivani 31304 Jun 1 15:10 posre.itp > -rw-rw-r-- 1 shivani shivani 576928 Jun 1 15:10 topol.top > [shivani@POLY3 tut1]$ > > Can you help me in fixing the same . > > Thanks > Regards > Shivani > -- > 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. > -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- 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] Fwd: Lysosyme in water
Dear Gromacs I am new and a beginner to this system. I am trying to learn through tutorials for version 5. When i performed i got the following error . [shivani@POLY3 tut1]$ editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 1.0 -bt cubic -bash: editconf: command not found [shivani@POLY3 tut1]$ gmx editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 1.0 -bt cubic -bash: gmx: command not found [shivani@POLY3 tut1]$ gmx_mpi editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 1.0 -bt cubic -bash: gmx_mpi: command not found [shivani@POLY3 tut1]$ gmpp editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 1.0 -bt cubic -bash: gmpp: command not found [shivani@POLY3 tut1]$ ls 1AKI.pdb 1AKI_processed.gro posre.itp topol.top [shivani@POLY3 tut1]$ ll total 812 -rw-rw-r-- 1 shivani shivani 116316 Jun 1 15:24 1AKI.pdb -rw-rw-r-- 1 shivani shivani 98776 Jun 1 15:10 1AKI_processed.gro -rw-rw-r-- 1 shivani shivani 31304 Jun 1 15:10 posre.itp -rw-rw-r-- 1 shivani shivani 576928 Jun 1 15:10 topol.top [shivani@POLY3 tut1]$ Can you help me in fixing the same . Thanks Regards Shivani -- 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] Fwd: tetrahedral order parameter
-- Forwarded message -- From: ISHRAT JAHAN Date: Fri, Jun 2, 2017 at 10:29 AM Subject: Re: [gmx-users] tetrahedral order parameter To: gmx-us...@gromacs.org I have used gmx hydorder but unable to understand the output as it gives two .xpm and two .out file. what these file describe , will you please explain it as i am newer to gromacs. Thanks in advance On Thu, Jun 1, 2017 at 6:14 PM, Justin Lemkul wrote: > > > On 6/1/17 3:42 AM, ISHRAT JAHAN wrote: > >> Dear all, >> I want to calculate tetrahedral order parameter of water molecule.can >> anyone tell me how to calculate it. >> > > Use gmx hydorder > > -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] QM/MM with Orca
Hi all, I have managed to compile Gromacs (2016 and 5.0.7) and run a simple QM/MM calculation with Orca as the QM engine, a MD run for a small peptide in vacuum. (If anyone is interested, I can share the procedure, adapted from a tutorial I found on the web.) However, the question I have is not specific to the Gromacs/Orca combination, but a bit more general. Now I'd like to solvate the peptide in water and perform a QM/MM run. It seems fairly simple if all water molecules are treated classically (please correct me if I'm wrong): the peptide will be QM, the waters are MM and no link atoms will be necessary. The coupling between the two regions will be handled by Gromacs and Orca via the polarization of the QM region by point charges and LJ. Am I right? Now, if the some of the water molecules are to be treated quantum-mechanically, there's the problem of molecules crossing the boundary of the quantum region. With a Google search, I stumbled upon the FIRES method (Salahub et al, Molecules 2015, 20, 4780-4812, doi: 10.3390/molecules20034780), which uses restraints (a simple quadratic potential) for keeping QM water molecules within a certain sphere around the QM molecule inside the sphere, while keeping MM molecules outside it. Is this method implemented in Gromacs, or could it be implemented for the QM and MM water molecules via specification of restraints in the .itp files? Thanks in advance, Marcos -- 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] RMSD Matrix error
Hi, On Sun, Jun 4, 2017 at 4:08 PM Apramita Chand wrote: > Dear All, > > When I'm trying to construct a RMSD matrix , using the command > g_rms -s protein_equili.gro -f protein_model1_ut.xtc -m > rmsd-matrix.xpm -tu ns > > I get the error: > Last frame 20 time 20.000 > > Building RMSD matrix, 21x21 elements > element 28982; time 2.90 Killed > That matrix has 4x10^10 elements, each of which needs 4 bytes of memory. 1GB is about 1x10^9 bytes, so you'd need at least 160 GB of memory. The real issue is that you are probably using a large number of highly correlated frames, so even if you could form the full distance matrix, you would not learn any more than you would from a matrix formed from a suitable sub-sampling. > I have given the reference structure to be the one prior to production run > and after equilibration step. I have also tried the command with .tpr file. > Same error! > The problem doesn't change with the nature of the reference structure. Mark > How to solve this? > > > yours sincerely > Apramita > -- > 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] Negative deuterium order parameters
Hello: I made 5 simulation: pure DPPC+a molecule inside, pure DPPE+molecule inside, 50% DPPC-50% DPPE+molecule inside, 75% DPPC-25%DPPE+molecule inside and 25%DPPC-75% DPPE+molecule inside. All the graphics were fine, but when i plot my system with 25%DPPC-755DPPE+Molecule inside the graphic of deuterium order parameters is not in order, is very disordered, with negative and positive values. Is it possible the molecule modifies the deuterium order parameters when i increase the DPPE %? Does anybody knows a reference i can read about this? Thanks. -- 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] Difference in properties when method of adding urea molecules is changed in a simulation box
Hi, Further, I would measure the distribution of the lifetime of hydrogen bonds, since you need to sample much longer than eg the average. And you should also try to measure the autocorrelation time of the number of hydrogen bonds - you don't have a "new" observation until you've simulated at least that long. Those will probably point to the fact that you aren't comparing the long sampling time limit in either case. Mark On Sun, 4 Jun 2017 18:39 André Farias de Moura wrote: > Hi Apramita, > > you have not told us how many urea molecules you have added to you system, > neither have you told how large your peptide of interest is, but usually > people studying denaturation of peptides use very concentrated urea > solutions (typically 8 M or so), which are highly viscous. > > If this is your case, 10 ns is certainly too short for equilibration and 20 > ns is also way too short for structural sampling, I would increase both by > maybe 5-10 fold longer if proper relaxation and sampling are expected (how > long is long enough can be monitored by the time evolution of the > properties of interest - only when plateaus are obtained you can begin the > production run) > > Andre > > > On Sun, Jun 4, 2017 at 12:39 PM, Apramita Chand > wrote: > > > Dear All, > > > > I have tested with two ways of solvating a peptide with urea-water > mixture > > Method 1: Pre-equilibrating a urea-water box and solvating the peptide > with > > -cs option with this box > > > > Method 2: Adding urea molecules to peptide box using -ci option and then > > solvating the resulting box with water molecules > > > > In both the methods, same number of urea and water molecules were added . > > 10ns equilibration followed by 20ns simulation steps were carried out. > > On analysing the properties, average number of hydrogen bonds between > > peptide-water in method 1 was 16.221 while it changed to 14.340 in Method > > 2. Similarly, number of H-bonds between peptide-urea changed from 5.687 > to > > 4.031 on switching from Method 1 to Method 2. > > > > On checking radial distribution functions, interaction between > > water-peptide sites were somewhat similar for both Methods but > significant > > changes were found for peptide-urea site-site correlations. Method-1 > showed > > higher peptide-urea interaction. > > > > What could be the reason for these discrepancies? Are both methods > correct? > > I want to go on with Method-2 for further simulations because it is > > relatively simpler but Method-1 shows higher hydrogen bonding between > > sites. > > > > Please suggest. > > > > yours sincerely, > > Apramita > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > -- > _ > > Prof. Dr. André Farias de Moura > Department of Chemistry > Federal University of São Carlos > São Carlos - Brazil > phone: +55-16-3351-8090 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- 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] Difference in properties when method of adding urea molecules is changed in a simulation box
Hi Apramita, you have not told us how many urea molecules you have added to you system, neither have you told how large your peptide of interest is, but usually people studying denaturation of peptides use very concentrated urea solutions (typically 8 M or so), which are highly viscous. If this is your case, 10 ns is certainly too short for equilibration and 20 ns is also way too short for structural sampling, I would increase both by maybe 5-10 fold longer if proper relaxation and sampling are expected (how long is long enough can be monitored by the time evolution of the properties of interest - only when plateaus are obtained you can begin the production run) Andre On Sun, Jun 4, 2017 at 12:39 PM, Apramita Chand wrote: > Dear All, > > I have tested with two ways of solvating a peptide with urea-water mixture > Method 1: Pre-equilibrating a urea-water box and solvating the peptide with > -cs option with this box > > Method 2: Adding urea molecules to peptide box using -ci option and then > solvating the resulting box with water molecules > > In both the methods, same number of urea and water molecules were added . > 10ns equilibration followed by 20ns simulation steps were carried out. > On analysing the properties, average number of hydrogen bonds between > peptide-water in method 1 was 16.221 while it changed to 14.340 in Method > 2. Similarly, number of H-bonds between peptide-urea changed from 5.687 to > 4.031 on switching from Method 1 to Method 2. > > On checking radial distribution functions, interaction between > water-peptide sites were somewhat similar for both Methods but significant > changes were found for peptide-urea site-site correlations. Method-1 showed > higher peptide-urea interaction. > > What could be the reason for these discrepancies? Are both methods correct? > I want to go on with Method-2 for further simulations because it is > relatively simpler but Method-1 shows higher hydrogen bonding between > sites. > > Please suggest. > > yours sincerely, > Apramita > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Difference in properties when method of adding urea molecules is changed in a simulation box
Dear All, I have tested with two ways of solvating a peptide with urea-water mixture Method 1: Pre-equilibrating a urea-water box and solvating the peptide with -cs option with this box Method 2: Adding urea molecules to peptide box using -ci option and then solvating the resulting box with water molecules In both the methods, same number of urea and water molecules were added . 10ns equilibration followed by 20ns simulation steps were carried out. On analysing the properties, average number of hydrogen bonds between peptide-water in method 1 was 16.221 while it changed to 14.340 in Method 2. Similarly, number of H-bonds between peptide-urea changed from 5.687 to 4.031 on switching from Method 1 to Method 2. On checking radial distribution functions, interaction between water-peptide sites were somewhat similar for both Methods but significant changes were found for peptide-urea site-site correlations. Method-1 showed higher peptide-urea interaction. What could be the reason for these discrepancies? Are both methods correct? I want to go on with Method-2 for further simulations because it is relatively simpler but Method-1 shows higher hydrogen bonding between sites. Please suggest. yours sincerely, Apramita -- 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] EM error
Can anyone please help me? Mohammad From: Mohammad Roostaie To: "gmx-us...@gromacs.org" Sent: Wednesday, 31 May 2017, 8:27:59 Subject: EM error Hi All, I wanted to run energy minimization process by this command: gmx mdrun -v -deffnm em. But, I got this error: tMPI error: malloc failure in tMPI (out of memory) (in valid comm)Aborted I do not know what the problem exactly is. Can you please help me? Thanks,Mohammad -- 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] RMSD Matrix error
Dear All, When I'm trying to construct a RMSD matrix , using the command g_rms -s protein_equili.gro -f protein_model1_ut.xtc -m rmsd-matrix.xpm -tu ns I get the error: Last frame 20 time 20.000 Building RMSD matrix, 21x21 elements element 28982; time 2.90 Killed I have given the reference structure to be the one prior to production run and after equilibration step. I have also tried the command with .tpr file. Same error! How to solve this? yours sincerely Apramita -- 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.
