Re: [gmx-users] 5ns simulation in 2 hours
Also check your time step size. A large time step can lead to numerical errors, but you will run more ns/day On Thu, Oct 29, 2015 at 8:56 AM, Smith, Micholas D. wrote: > A few clairfying questions: > > 1) What is the size of the system? > 2) What is your frame saving rate? > 3) Are you using a GPU? What about MPI or OpenMP? > > 60ns a day (what 5ns/2hours) is not unheard of given a reasonable system > size and GPU acceleration. If you are curious about the performance you can > always check your log files and see what is going on. > > -Micholas > > === > Micholas Dean Smith, PhD. > Post-doctoral Research Associate > University of Tennessee/Oak Ridge National Laboratory > Center for Molecular Biophysics > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Sana > Saeed > Sent: Wednesday, October 28, 2015 11:24 PM > To: gromacs.org_gmx-users > Subject: [gmx-users] 5ns simulation in 2 hours > > hi gmx users!i run 5 ns simulation and it took only 2 hours..is it > possible? its showing no error.. > Regards Autumn > -- > 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] GROMACS http download?
I can't access the tar.gz at http://www.gromacs.org/Downloads because it is on FTP, which my (corporate) proxy blocks. Is there an http mirror where I can download these files? I need to download these: ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.5.tar.gz ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.7.tar.gz ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.5.tar.gz Thanks in advance. --- [http://5.cim.co.cu/cim.gif] -- 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] Resuming GROMACS simulation in a different computer?
Suppose I have a GROMACS simulation that was running on a computer with a given number of processors. This run was interrupted for some reason. Now I want to resume it by using the checkpoint .ctp file, but I want to resume it in a different computer. The second computer can have a different number of processors that the first computer, different RAM, etc. Is this safe? --- [http://5.cim.co.cu/cim.gif] -- 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] Respect waters in crystallographic pdb file?
Hi all, I have a crystallographic PDB file which comes some waters molecules. I want to run an MD simulation which includes those water molecules. After generating the topology file (which includes the waters) and defining the box shape, I fill the box with solvent using genbox. At this point it becomes impossible to track down visually where the water molecules are. My question is if the file that genbox outputs still contains the crystallographic water molecules? Or are they replaced by the molecules added by genbox? Thanks in advance. Best, cossio --- [http://5.cim.co.cu/cim.gif] -- 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] Respect waters in crystallographic pdb file?
And what about genion? Suppose I have to add some ions to the system to neutralize, so I use the following command: genion -s S_ion.tpr -o S_sol.gro -p S_sol.top -nn 1 -nname CL <<<"SOL" Is there a chance that this replaces one of the original crytallographic waters with the CL? Thanks. Best, cossio -- Message: 2 Date: Mon, 17 Aug 2015 14:14:28 -0400 From: Justin Lemkul To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Respect waters in crystallographic pdb file? Message-ID: <55d22484.9030...@vt.edu> Content-Type: text/plain; charset=windows-1252; format=flowed They should be in the same place they always were (unless you've modified the box dimensions, in which case the coordinates of everything get changed). But genbox shouldn't delete waters that were already present. The crystallographic waters should always be the first ones written after e.g. the protein. -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 ====== On 8/17/15 1:42 PM, Jorge Fernandez de Cossio Diaz wrote: > Hi all, I have a crystallographic PDB file which comes some waters molecules. > I want to run an MD simulation which includes those water molecules. After > generating the topology file (which includes the waters) and defining the box > shape, I fill the box with solvent using genbox. At this point it becomes > impossible to track down visually where the water molecules are. My question > is if the file that genbox outputs still contains the crystallographic water > molecules? Or are they replaced by the molecules added by genbox? Thanks in --- [http://5.cim.co.cu/cim.gif] -- 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] Broken protein chain: "WARNING: Listed nonbonded interaction between particles ..."
Hi all, I have a PDB file containing two proteins. One of the proteins has a long stretch of missing residues. When I try to energy-minimize it, I get the following: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm. Now, it turns out that atoms 2897 and 2908 belong to the residues between which the missing sequence lies. They are very far apart (because the missing stretch is quite long), so I don't think there should be any interaction between them. However, this WARNING seems to be saying that for some reason, the topology generated included an interaction between them, probably because it interpreted that since the two residues are consecutive in the PDB file, they are bonded (which they aren't, because of the missing residues). After trying some things, I realized that if I remove the option "-chainsep id" from pdb2gmx when I generate the topology, I don't get this warning. Instead, I get a bunch of topology files, each corresponding to a fragment of each chain, instead of a topology per chain. This is very hard to deal with, because, for example, if I want to make a position restrain on the backbone of each chain, I have to keep track of each fragment separately. Is there a way to fix the WARNING above without having to remove the option "-chainsep id" from pdb2gmx? Thanks. Best, cossio --- [http://5.cim.co.cu/cim.gif] -- 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] What's the point of adding ions to neutralize the system?
Since the ion added is usually very far away from the protein (or molecule of interest), I don't see how it can affect the results of the molecular dynamics simulation. So why is it so important to add ions to neutralize the net-charge of the system? --- [http://5.cim.co.cu/cim.gif] -- 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] Broken protein chain: "WARNING: Listed nonbonded interaction between particles ..."
Tried using -merge interactive -chainsep id on pdb2gmx, but I still get the same WARNING: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm. The energy minimization step prints this as a warning and proceeds, but when I try to equilibrate the system later, the warning becomes an error and it doesn't let me proceed, so this seems to be important. Also, it doesn't make sense to me that 2897 and 2908 are interacting, because even though they are consecutive (because of missing residues), they are very far apart in space. So why is it that when I put the fragments into the same chain, the topology creates this spurious interaction? -- Message: 4 Date: Thu, 20 Aug 2015 19:00:29 + From: Mark Abraham To: gmx-us...@gromacs.org, "gromacs.org_gmx-users@maillist.sys.kth.se" Subject: Re: [gmx-users] Broken protein chain: "WARNING: Listed nonbonded interaction between particles ..." Message-ID: Content-Type: text/plain; charset=UTF-8 Hi, Yes, see pdbgmx -h about merge. Probably you want -merge interactive -chainsep id Mark On Thu, Aug 20, 2015 at 8:39 PM Jorge Fernandez de Cossio Diaz < cos...@cim.sld.cu> wrote: > Hi all, > > I have a PDB file containing two proteins. One of the proteins has a long > stretch of missing residues. When I try to energy-minimize it, I get the > following: > > WARNING: Listed nonbonded interaction between particles 2897 and 2908 > at distance 3f which is larger than the table limit 3f nm. > > Now, it turns out that atoms 2897 and 2908 belong to the residues between > which the missing sequence lies. They are very far apart (because the > missing stretch is quite long), so I don't think there should be any > interaction between them. However, this WARNING seems to be saying that for > some reason, the topology generated included an interaction between them, > probably because it interpreted that since the two residues are consecutive > in the PDB file, they are bonded (which they aren't, because of the missing > residues). > > After trying some things, I realized that if I remove the option > "-chainsep id" from pdb2gmx when I generate the topology, I don't get this > warning. Instead, I get a bunch of topology files, each corresponding to a > fragment of each chain, instead of a topology per chain. This is very hard > to deal with, because, for example, if I want to make a position restrain > on the backbone of each chain, I have to keep track of each fragment > separately. > > Is there a way to fix the WARNING above without having to remove the > option "-chainsep id" from pdb2gmx? > > Thanks. Best, > cossio > --- --- [http://5.cim.co.cu/cim.gif] -- 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] Broken protein chain: "WARNING: Listed nonbonded
Note that I am adding position restrains to fix all the termini of the incomplete fragments. Shouldn't that take care of the missing residues? -- Message: 5 Date: Thu, 20 Aug 2015 20:29:42 + From: Jorge Fernandez de Cossio Diaz To: "gromacs.org_gmx-users@maillist.sys.kth.se" Subject: Re: [gmx-users] Broken protein chain: "WARNING: Listed nonbonded interaction between particles ..." Message-ID: Content-Type: text/plain; charset="us-ascii" Tried using -merge interactive -chainsep id on pdb2gmx, but I still get the same WARNING: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm. The energy minimization step prints this as a warning and proceeds, but when I try to equilibrate the system later, the warning becomes an error and it doesn't let me proceed, so this seems to be important. Also, it doesn't make sense to me that 2897 and 2908 are interacting, because even though they are consecutive (because of missing residues), they are very far apart in space. So why is it that when I put the fragments into the same chain, the topology creates this spurious interaction? -- Message: 4 Date: Thu, 20 Aug 2015 19:00:29 + From: Mark Abraham To: gmx-us...@gromacs.org, "gromacs.org_gmx-users@maillist.sys.kth.se" Subject: Re: [gmx-users] Broken protein chain: "WARNING: Listed nonbonded interaction between particles ..." Message-ID: Content-Type: text/plain; charset=UTF-8 Hi, Yes, see pdbgmx -h about merge. Probably you want -merge interactive -chainsep id Mark On Thu, Aug 20, 2015 at 8:39 PM Jorge Fernandez de Cossio Diaz < cos...@cim.sld.cu> wrote: > Hi all, > > I have a PDB file containing two proteins. One of the proteins has a long > stretch of missing residues. When I try to energy-minimize it, I get the > following: > > WARNING: Listed nonbonded interaction between particles 2897 and 2908 > at distance 3f which is larger than the table limit 3f nm. > > Now, it turns out that atoms 2897 and 2908 belong to the residues between > which the missing sequence lies. They are very far apart (because the > missing stretch is quite long), so I don't think there should be any > interaction between them. However, this WARNING seems to be saying that for > some reason, the topology generated included an interaction between them, > probably because it interpreted that since the two residues are consecutive > in the PDB file, they are bonded (which they aren't, because of the missing > residues). > > After trying some things, I realized that if I remove the option > "-chainsep id" from pdb2gmx when I generate the topology, I don't get this > warning. Instead, I get a bunch of topology files, each corresponding to a > fragment of each chain, instead of a topology per chain. This is very hard > to deal with, because, for example, if I want to make a position restrain > on the backbone of each chain, I have to keep track of each fragment > separately. > > Is there a way to fix the WARNING above without having to remove the > option "-chainsep id" from pdb2gmx? > > Thanks. Best, > cossio > --- --- [http://5.cim.co.cu/cim.gif] -- Message: 6 Date: Thu, 20 Aug 2015 16:40:27 -0400 From: Justin Lemkul To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Broken protein chain: "WARNING: Listed nonbonded interaction between particles ..." Message-ID: <55d63b3b.6040...@vt.edu> Content-Type: text/plain; charset=windows-1252; format=flowed On 8/20/15 4:29 PM, Jorge Fernandez de Cossio Diaz wrote: > Tried using -merge interactive -chainsep id on pdb2gmx, but I still get the > same WARNING: > > WARNING: Listed nonbonded interaction between particles 2897 and 2908 > at distance 3f which is larger than the table limit 3f nm. > > The energy minimization step prints this as a warning and proceeds, but when > I try to equilibrate the system later, the warning becomes an error and it > doesn't let me proceed, so this seems to be important. Also, it doesn't make > sense to me that 2897 and 2908 are interacting, because even though they are > consecutive (because of missing residues), they are very far apart in space. > > So why is it that when I put the fragments into the same chain, the topology > creates this spurious interaction? > Because you're ignoring something physically relevant - you have missing residues! pdb2gmx certainly gave "long bond" warnings when you produced the topology. You need to model in t
