Re: [gmx-users] Energy minimisation goes to several values
Thanks Justin for the reply. Honestly I thought minimizing a large and complex (usually biomolecular) system part by part instead of as a whole will effectively shorten the computational time cost while causing no effect on the final structure. When you say “impedes”, do you mean it causes a longer calculation time in total or it will give a bad final structure? Thanks in advance, Kevin On 26 Jun, 2015, at 22:21, gromacs.org_gmx-users-requ...@maillist.sys.kth.se gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: From: Justin Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] Energy minimisation goes to several values Date: 26 June, 2015 21:27:32 HKT To: gmx-us...@gromacs.org mailto:gmx-us...@gromacs.org Reply-To: gmx-us...@gromacs.org mailto:gmx-us...@gromacs.org On 6/25/15 9:45 PM, Kevin C Chan wrote: Dear Users, I am energy minimising a quite large solvated system containing protein and lipids (~800,000 atoms). I used to fix components of the system in order to speed-up energy minimisation and sometimes it is easier to debug such processes. Here is my protocol: 1. fix all except water and so to minimise water 2. fix water and then minimise all the rest atoms 3. fix nothin and then minimise the whole system While monitoring the energy of the system thought minimisations, it goes fine for step 1 and 2 and converged after just few hundred steps. However it goes back to several higher values of energy (bouncing between the values) and they started to increase very slowly for step 3. This makes no sense to me and did anyone have a similar experience? There are two unusual points: 1. The system energy drops suddenly instead of decreased gradually during step2 and then stays at a constant value. 2. If I use the resulting structure from step3 to proceed a, say, heating process, it simply blows up. To be clear, my system was solvated and auto-ionized using VMD tools and some water inside the membrane has been directly deleted. Backbone of the protein and phosphorus atoms of the membrane are under a position constraint during all the minimisations. I was choosing conjugate gradient for minimization. Does a normal minimization (just one overall minimization with nothing fixed) yield a stable starting point? Fixing atoms (using freezegrps?) often actually impedes minimization. -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 mailto:jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul 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] error gcq#360
On 6/26/15 9:15 AM, Urszula Uciechowska wrote: Dear gmx users, after running grompp -f em.mdp -c COM_ions.gro -p COM.top -o em.tpr I obtained: GROMACS: gmx grompp, VERSION 5.0 Executable: /software/local/el6/INTEL/gromacs/5.0.0/intel-ompi-fftw-blas-lapack/bin/gmx Library dir: /software/local/el6/INTEL/gromacs/5.0.0/intel-ompi-fftw-blas-lapack/share/gromacs/top Command line: grompp -f em.mdp -c COM_ions.gro -p COM.top -o em.tpr Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# Setting the LD random seed to 2993272762 Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'DNA' Excluding 3 bonded neighbours molecule type 'DNA2' Excluding 3 bonded neighbours molecule type 'Protein3' Excluding 3 bonded neighbours molecule type 'Protein4' Excluding 3 bonded neighbours molecule type 'Protein5' Excluding 3 bonded neighbours molecule type 'Protein6' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 1 bonded neighbours molecule type 'NA' Excluding 1 bonded neighbours molecule type 'CL' Removing all charge groups because cutoff-scheme=Verlet Analysing residue names: There are: 136DNA residues There are: 1140Protein residues There are: 557197 Water residues There are: 2152Ion residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 5090256.00 Calculating fourier grid dimensions for X Y Z Using a fourier grid of 216x216x216, spacing 0.119 0.119 0.119 Estimate for the relative computational load of the PME mesh part: 0.27 NOTE 1 [file em.mdp]: This run will generate roughly 586540 Mb of data There was 1 note gcq#360: error: too many template-parameter-lists (g++) At the end I have em.tpr file but I am not sure if everything is ok. Any suggestions. gcq are GROMACS cool quotes and serve no functional purpose except the amusement of the user. There is no error here. -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] Configuration bug preventing GROMACS 5.0 build with Intel compiler?
Hi, I haven't tried to build with IntelMPI for a while, but we might consider patches to work around issues. Depends how ugly they make the things that are not broken :-) Perhaps Roland has experience here? Mark On Fri, Jun 26, 2015 at 3:37 PM Åke Sandgren ake.sandg...@hpc2n.umu.se wrote: Just noticed this question from Sep 2014. The problem was that configuring with the Intel compiler and IntelMPI causes incorrect detection of _finite. This is caused by bugs in the IntelMPI wrappers for both gcc and intel compilers, including the MIC wrappers. I have patches available if someone want to have them. I have not had time to report this to Intel yet... -- Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden Internet: a...@hpc2n.umu.se Phone: +46 90 7866134 Fax: +46 90-580 14 Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se -- 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] The pullf.xvg and pullx.xvg files
Dear Justin, I have done two parallel short pullings, one with pull_geometry = cylinder and one with pull_geometry = direction. When pull_geometry = direction, everything works perfectly: the grompp output says that the distance at start, as well as the reference at t=0 are both equal to 3.019 nm, and the pullx.xvg file reflects this: at t=0 the distance is also 3.019 nm. This distance is reasonable based on my geometry. The force at t=0 is 10^-6 and the COM pull energy in the md.log file is on the order of 10^-10. When pull_geometry = cylinder, the grompp output says the distance at start and the reference distance are 1.215 nm (which they aren't) but the distance at t=0 in the pullx.xvg file shows up as 2.8 nm (which it is roughly - it's hard to tell where the COM as computed by the cylinder approach would be but it is likely to be close to the COM as usually computed). This huge discrepancy leads to huge forces as well as energies at t=0. Is this some kind of bug that has been fixed since Gromacs 5.0.2, which is the version I'm using, or should I report it? I think since the distance computed by grompp and that in the pullx.xvg file at t=0 are different, the method will likely give inaccurate forces and thus PMF's... What do you think? Laura On Thu, Jun 25, 2015 at 11:07 AM, Laura Tociu lto...@princeton.edu wrote: Ok thanks! I will analyze this more deeply and maybe also try differen geometries. And sorry for the stupid question, I was reading force but was thinking potential instead... Laura -- From: Justin Lemkul jalem...@vt.edu Sent: 25/06/2015 02:23 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] The pullf.xvg and pullx.xvg files On 6/24/15 9:20 AM, Laura Tociu wrote: Dear Justin, Thanks for the reply! Yeah, I understand how the pulling works now. The forces at time t=0 are not zero, though. There are huge forces such as -270 or even -1700 kj/mol/nm acting on my pull group at time t=0. What do you believe could be the cause of that? And why is there a /nm in that force? I mean, isn't the force per nm (force constant) of the spring always 1000 kj/mol/nm, but the actual force adopts various different values as time goes by? The force constant is in kJ/mol/nm^2 (same as all bonded force constants). Force is kJ/mol/nm because force is the negative derivative of potential with respect to position. You can also convert this rather easily to pN or some more familiar unit. I ran a short simulation with pull_coord1_rate = 0, and when I did that I got reasonable forces such as 40-60 kj/mol/nm (??) but still not a zero force at time t=0. Please let me know if this is normal behavior or not. Sorry, can't tell without fully analyzing all of your files (not something I have time for). Check what grompp reports as the reference distance at t=0 vs. what you calculate in the input coordinate file/first frame of the trajectory. I've never used the cylinder geometry; could be something specific to that. -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.
Re: [gmx-users] problem to restart REMD
Hi, I can't tell what you've done so that md0.log doesn't match, but that's why I suggested you make a backup. You also don't have to have appending, that's just for convenience. The advice about node count mismatch doesn't matter here... Use your judgement! Mark On Thu, 25 Jun 2015 16:23 leila salimi leilasal...@gmail.com wrote: Thanks very much. Ok I will check again, it seems that they are at the same step! only the thing that comes to my mind is that I used different number of cpus when I tried to update few steps for some replicas, and then I used the primary numbers of cpu that I used. Also I got this error when I update it the some state.cpt Fatal error: Checksum wrong for 'md0.log'. The file has been replaced or its contents have been modified. Cannot do appending because of this condition. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors and also this! #nodes mismatch, current program: 2 checkpoint file: 128 #PME-nodes mismatch, current program: -1 checkpoint file: 32 I hope to figure out this problem, otherwise I have to run it from beginning! Thanks! Leila On Thu, Jun 25, 2015 at 4:15 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, I can't tell either. Please run gmxcheck on all your input files, to check the simulation part, time and step number are all what you think they are (and that they match across the simulations) and try again. Mark On Thu, Jun 25, 2015 at 4:12 PM leila salimi leilasal...@gmail.com wrote: Dear Mark, When I tried with new update of the state.cpt files, I got this error. Abort(1) on node 896 (rank 896 in comm 1140850688): Fatal error in MPI_Allreduce: Message truncated, error stack: MPI_Allreduce(912)...: MPI_Allreduce(sbuf=MPI_IN_PLACE, rbuf=0x7ffc783af760, count=4, MPI_DOUBLE, MPI_SUM, comm=0x8402) failed MPIR_Allreduce_impl(769).: MPIR_Allreduce_intra(419): MPIC_Sendrecv(467)...: MPIDI_Buffer_copy(73): Message truncated; 64 bytes received but buffer size is 32 Abort(1) on node 768 (rank 768 in comm 1140850688): Fatal error in MPI_Allreduce: Message truncated, error stack: MPI_Allreduce(912)...: MPI_Allreduce(sbuf=MPI_IN_PLACE, rbuf=0x7ffdba5176a0, count=4, MPI_DOUBLE, MPI_SUM, comm=0x8402) failed MPIR_Allreduce_impl(769).: MPIR_Allreduce_intra(419): MPIC_Sendrecv(467)...: MPIDI_Buffer_copy(73): Message truncated; 64 bytes received but buffer size is 32 ERROR: 0031-300 Forcing all remote tasks to exit due to exit code 1 in task 896 job.err.1011016.out 399L, 17608C Actually I don't know what is the problem! Regards, Leila On Thu, Jun 18, 2015 at 12:00 AM, leila salimi leilasal...@gmail.com wrote: I understand what you meant, I run only few steps for the other replicas and then continue with the whole replicas. I hope every thing is going well. Thanks very much. On Wed, Jun 17, 2015 at 11:43 PM, leila salimi leilasal...@gmail.com wrote: Thanks Mark for your suggestion. Actually I don't understand the new two state6.cpt and state7,cpt files, because the time that it shows is 127670.062 ! That is strange! because my time step is 2 fs and I saved the output every 250 steps, means every 500 fs. I expect the time should be like 127670.000 or 127670.500 . By the way you mean with mdrun_mpi ... -nsteps ... , I can get the steps that I need for the old state.cpt files? Regards, Leila On Wed, Jun 17, 2015 at 11:22 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, That's all extremely strange. Given that you aren't going to exchange in that short period of time, you can probably do some arithmetic and work out how many steps you'd need to advance whichever set of files is behind the other. Then mdrun_mpi ... -nsteps y can write a set of checkpoint files that will be all at the same time! Mark On Wed, Jun 17, 2015 at 10:18 PM leila salimi leilasal...@gmail.com wrote: Hi Mark, Thanks very much. Unfortunately both the state6.cpt, state6_prev,cpt and state7.cpt and state7_prev.cpt updated and their time are different from other replicas file (also with *_prev.cpt )! I am thinking maybe I can use init-step in mdp file, and start from the time that I have, because all trr files have the same time! I checked with gmxcheck. But I am not sure that I will get correct results! Actually I got confused that with the mentioned Note, only two replicas were running and the state file is changed and the others not! regards, Leila -- Gromacs Users mailing list * Please search the archive at
Re: [gmx-users] problem to restart REMD
Actually when I check for several times I checked the steps for all state.cpt files and they are the same. I try to restart it, it is run only for few steps ( It took only 3 minutes ) and then it stopped with this lines in the error file : Abort(1) on node 12 (rank 12 in comm 1140850688): Fatal error in MPI_Allreduce: Other MPI error, error stack: MPI_Allreduce(912)...: MPI_Allreduce(sbuf=MPI_IN_PLACE, rbuf=0x7fff8606aa00, count=4, MPI_DOUBLE, MPI_SUM, comm=0x8401) failed MPIR_Allreduce_impl(769).: MPIR_Allreduce_intra(270): MPIR_Bcast_impl(1462): MPIR_Bcast(1486).: MPIR_Bcast_intra(1295)...: MPIR_Bcast_binomial(252).: message sizes do not match across processes in the collective routine: Received 64 but expected 32 ERROR: 0031-300 Forcing all remote tasks to exit due to exit code 1 in task 12 That I guess the problem is related to MPI, and I don't get why, because my other simulation is running well. Thanks for your suggestion. Leila On Fri, Jun 26, 2015 at 7:10 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, I can't tell what you've done so that md0.log doesn't match, but that's why I suggested you make a backup. You also don't have to have appending, that's just for convenience. The advice about node count mismatch doesn't matter here... Use your judgement! Mark On Thu, 25 Jun 2015 16:23 leila salimi leilasal...@gmail.com wrote: Thanks very much. Ok I will check again, it seems that they are at the same step! only the thing that comes to my mind is that I used different number of cpus when I tried to update few steps for some replicas, and then I used the primary numbers of cpu that I used. Also I got this error when I update it the some state.cpt Fatal error: Checksum wrong for 'md0.log'. The file has been replaced or its contents have been modified. Cannot do appending because of this condition. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors and also this! #nodes mismatch, current program: 2 checkpoint file: 128 #PME-nodes mismatch, current program: -1 checkpoint file: 32 I hope to figure out this problem, otherwise I have to run it from beginning! Thanks! Leila On Thu, Jun 25, 2015 at 4:15 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, I can't tell either. Please run gmxcheck on all your input files, to check the simulation part, time and step number are all what you think they are (and that they match across the simulations) and try again. Mark On Thu, Jun 25, 2015 at 4:12 PM leila salimi leilasal...@gmail.com wrote: Dear Mark, When I tried with new update of the state.cpt files, I got this error. Abort(1) on node 896 (rank 896 in comm 1140850688): Fatal error in MPI_Allreduce: Message truncated, error stack: MPI_Allreduce(912)...: MPI_Allreduce(sbuf=MPI_IN_PLACE, rbuf=0x7ffc783af760, count=4, MPI_DOUBLE, MPI_SUM, comm=0x8402) failed MPIR_Allreduce_impl(769).: MPIR_Allreduce_intra(419): MPIC_Sendrecv(467)...: MPIDI_Buffer_copy(73): Message truncated; 64 bytes received but buffer size is 32 Abort(1) on node 768 (rank 768 in comm 1140850688): Fatal error in MPI_Allreduce: Message truncated, error stack: MPI_Allreduce(912)...: MPI_Allreduce(sbuf=MPI_IN_PLACE, rbuf=0x7ffdba5176a0, count=4, MPI_DOUBLE, MPI_SUM, comm=0x8402) failed MPIR_Allreduce_impl(769).: MPIR_Allreduce_intra(419): MPIC_Sendrecv(467)...: MPIDI_Buffer_copy(73): Message truncated; 64 bytes received but buffer size is 32 ERROR: 0031-300 Forcing all remote tasks to exit due to exit code 1 in task 896 job.err.1011016.out 399L, 17608C Actually I don't know what is the problem! Regards, Leila On Thu, Jun 18, 2015 at 12:00 AM, leila salimi leilasal...@gmail.com wrote: I understand what you meant, I run only few steps for the other replicas and then continue with the whole replicas. I hope every thing is going well. Thanks very much. On Wed, Jun 17, 2015 at 11:43 PM, leila salimi leilasal...@gmail.com wrote: Thanks Mark for your suggestion. Actually I don't understand the new two state6.cpt and state7,cpt files, because the time that it shows is 127670.062 ! That is strange! because my time step is 2 fs and I saved the output every 250 steps, means every 500 fs. I expect the time should be like 127670.000 or 127670.500 . By the way you mean with mdrun_mpi ... -nsteps ... , I can get the steps that I need for the old state.cpt files? Regards, Leila On Wed, Jun 17, 2015 at 11:22 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, That's all
[gmx-users] pretty large coulomb contribution to free energy
Dear users, The free energy of decoupling the ligand from the complex I get is about 457 kcal/mol. If for ligand in solution I get -5 kcal/mol, and for the restraints -8 kcal/mol. Binding free energy is 457-5-8=444 kcal/mol. A value over 400-500 kcal/mol is not unexpected for decoupling the ligand from the complex? Anyone experienced similar problem? The problem is the intramolecular interaction of the ligand? How about this Gromacs version https://github.com/gromacs/gromacs/tree/022ad08b2fd0c1de085e88ac81a61841c4daea9c ? Ligand I used is neutral. Gromacs version is 4.6.5 Free energy control parts of my input files are below. For decoupling the ligand from the complex # ; Free energy control stuff init-lambda-state= 5 free_energy = yes sc-alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 restraint-lambdas= 0.0 0.01 0.025 0.05 0.075 0.1 0.2 0.35 0.5 0.75 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 coul-lambdas = 0.0 0.00 0.000 0.00 0.000 0.0 0.0 0.00 0.0 0.00 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 vdw-lambdas = 0.0 0.00 0.000 0.00 0.000 0.0 0.0 0.00 0.0 0.00 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0 nstdhdl = 10 pull = umbrella pull_geometry = distance pull_dim = Y Y Y pull_start = no pull_init1 = 0.2980769 pull_ngroups = 1 pull_group0= atom-p pull_group1= atom-l pull_k1= 0.0 ; kJ*mol^(-1)*nm^(-2) pull_kB1 = 4184 ; kJ*mol^(-1)*nm^(-2) For solvation free energy ### ; Free energy control stuff init-lambda-state= 5 free_energy = yes sc-alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 coul-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 vdw-lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0 nstdhdl = 10 couple-intramol = yes couple-moltype = MOL couple-lambda0 = vdw-q couple-lambda1 = none -- Ahmet Yıldırım -- 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] counting the number of water molecules surrounding proteins
Dear Gromacs Users
Hello.
I have a question about how to count the number of water molecules
surrounding protiens.
I have tried two methods and the results from two methods were different.
The first one is use g_trjorder -f structure.xtc -s structure.tpr -n
index.ndx -nshell water_in_0.22.xvg -r 0.22
I have chose first reference group as protein and second group water.
Using this method, I could calculate the number of water molecules in 0.22
nm as time from protein.
The second method is using mindist.
At first I have calcualted minimum distance from water to protien within
0.5 nm using g_mindist
g_mindist -s structure.tpr -f structure.xtc -n index.ndx -d 0.50
-respertime -od od.xvg -or mindrest.xvg
Here I chose the first reference group water and second reference group
protein. As long as I understand, mindrest.xvg include minimum distance
data of the water-protein per each water molecule.
And then using grep, I have extracted the number of water molecules in the
range of r0.22
grep -v '[#|@|S]' mindistres.xvg | awk '{a1=0;;for(i=2;i=NF;i++)
if($i'0.22') a1++;print $1,a1}' water_count.xvg
Then I could obtain the number of water molecules in 0.22 nm as a function
of time.
When I got time-averaged values of the number of water molecules within
0.22 nm, the value from first method is different from second method. I got
162 water molecules from first method, while I got 222 water molecules from
second one.
Does anyone have experience in this method?
Thanks,
Sang Eun Jee
Post Doctoral Researcher
School of Materials Science and Engineering
Georgia Institute of Technology
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mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] problem to restart REMD
Dear Micholas, I agree with you! I am trying to find what is wrong with restarting this system! I am sure that if I start from begging It will stop at this step and stuck! I checked every thing seems fine but REMD is not working! Now I am trying to run only the first 5 repilcas and to see that is it passing the step or not! I will tell you my finding. Leila On Fri, Jun 26, 2015 at 9:16 PM, Smith, Micholas D. smit...@ornl.gov wrote: Leila, your error is interesting, as I have had a very similar MPI_Allreduce error when I try to restart a large scale REMD. The first few times the system restarted just fine, but at somepoint it fails. Out of curiousity, if we try to re-run from the beginning does it work? -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 leila salimi leilasal...@gmail.com Sent: Friday, June 26, 2015 1:30 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] problem to restart REMD Actually when I check for several times I checked the steps for all state.cpt files and they are the same. I try to restart it, it is run only for few steps ( It took only 3 minutes ) and then it stopped with this lines in the error file : Abort(1) on node 12 (rank 12 in comm 1140850688): Fatal error in MPI_Allreduce: Other MPI error, error stack: MPI_Allreduce(912)...: MPI_Allreduce(sbuf=MPI_IN_PLACE, rbuf=0x7fff8606aa00, count=4, MPI_DOUBLE, MPI_SUM, comm=0x8401) failed MPIR_Allreduce_impl(769).: MPIR_Allreduce_intra(270): MPIR_Bcast_impl(1462): MPIR_Bcast(1486).: MPIR_Bcast_intra(1295)...: MPIR_Bcast_binomial(252).: message sizes do not match across processes in the collective routine: Received 64 but expected 32 ERROR: 0031-300 Forcing all remote tasks to exit due to exit code 1 in task 12 That I guess the problem is related to MPI, and I don't get why, because my other simulation is running well. Thanks for your suggestion. Leila On Fri, Jun 26, 2015 at 7:10 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, I can't tell what you've done so that md0.log doesn't match, but that's why I suggested you make a backup. You also don't have to have appending, that's just for convenience. The advice about node count mismatch doesn't matter here... Use your judgement! Mark On Thu, 25 Jun 2015 16:23 leila salimi leilasal...@gmail.com wrote: Thanks very much. Ok I will check again, it seems that they are at the same step! only the thing that comes to my mind is that I used different number of cpus when I tried to update few steps for some replicas, and then I used the primary numbers of cpu that I used. Also I got this error when I update it the some state.cpt Fatal error: Checksum wrong for 'md0.log'. The file has been replaced or its contents have been modified. Cannot do appending because of this condition. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors and also this! #nodes mismatch, current program: 2 checkpoint file: 128 #PME-nodes mismatch, current program: -1 checkpoint file: 32 I hope to figure out this problem, otherwise I have to run it from beginning! Thanks! Leila On Thu, Jun 25, 2015 at 4:15 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, I can't tell either. Please run gmxcheck on all your input files, to check the simulation part, time and step number are all what you think they are (and that they match across the simulations) and try again. Mark On Thu, Jun 25, 2015 at 4:12 PM leila salimi leilasal...@gmail.com wrote: Dear Mark, When I tried with new update of the state.cpt files, I got this error. Abort(1) on node 896 (rank 896 in comm 1140850688): Fatal error in MPI_Allreduce: Message truncated, error stack: MPI_Allreduce(912)...: MPI_Allreduce(sbuf=MPI_IN_PLACE, rbuf=0x7ffc783af760, count=4, MPI_DOUBLE, MPI_SUM, comm=0x8402) failed MPIR_Allreduce_impl(769).: MPIR_Allreduce_intra(419): MPIC_Sendrecv(467)...: MPIDI_Buffer_copy(73): Message truncated; 64 bytes received but buffer size is 32 Abort(1) on node 768 (rank 768 in comm 1140850688): Fatal error in MPI_Allreduce: Message truncated, error stack: MPI_Allreduce(912)...: MPI_Allreduce(sbuf=MPI_IN_PLACE, rbuf=0x7ffdba5176a0, count=4, MPI_DOUBLE, MPI_SUM, comm=0x8402) failed MPIR_Allreduce_impl(769).: MPIR_Allreduce_intra(419): MPIC_Sendrecv(467)...:
Re: [gmx-users] problem to restart REMD
Leila, your error is interesting, as I have had a very similar MPI_Allreduce error when I try to restart a large scale REMD. The first few times the system restarted just fine, but at somepoint it fails. Out of curiousity, if we try to re-run from the beginning does it work? -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 leila salimi leilasal...@gmail.com Sent: Friday, June 26, 2015 1:30 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] problem to restart REMD Actually when I check for several times I checked the steps for all state.cpt files and they are the same. I try to restart it, it is run only for few steps ( It took only 3 minutes ) and then it stopped with this lines in the error file : Abort(1) on node 12 (rank 12 in comm 1140850688): Fatal error in MPI_Allreduce: Other MPI error, error stack: MPI_Allreduce(912)...: MPI_Allreduce(sbuf=MPI_IN_PLACE, rbuf=0x7fff8606aa00, count=4, MPI_DOUBLE, MPI_SUM, comm=0x8401) failed MPIR_Allreduce_impl(769).: MPIR_Allreduce_intra(270): MPIR_Bcast_impl(1462): MPIR_Bcast(1486).: MPIR_Bcast_intra(1295)...: MPIR_Bcast_binomial(252).: message sizes do not match across processes in the collective routine: Received 64 but expected 32 ERROR: 0031-300 Forcing all remote tasks to exit due to exit code 1 in task 12 That I guess the problem is related to MPI, and I don't get why, because my other simulation is running well. Thanks for your suggestion. Leila On Fri, Jun 26, 2015 at 7:10 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, I can't tell what you've done so that md0.log doesn't match, but that's why I suggested you make a backup. You also don't have to have appending, that's just for convenience. The advice about node count mismatch doesn't matter here... Use your judgement! Mark On Thu, 25 Jun 2015 16:23 leila salimi leilasal...@gmail.com wrote: Thanks very much. Ok I will check again, it seems that they are at the same step! only the thing that comes to my mind is that I used different number of cpus when I tried to update few steps for some replicas, and then I used the primary numbers of cpu that I used. Also I got this error when I update it the some state.cpt Fatal error: Checksum wrong for 'md0.log'. The file has been replaced or its contents have been modified. Cannot do appending because of this condition. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors and also this! #nodes mismatch, current program: 2 checkpoint file: 128 #PME-nodes mismatch, current program: -1 checkpoint file: 32 I hope to figure out this problem, otherwise I have to run it from beginning! Thanks! Leila On Thu, Jun 25, 2015 at 4:15 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, I can't tell either. Please run gmxcheck on all your input files, to check the simulation part, time and step number are all what you think they are (and that they match across the simulations) and try again. Mark On Thu, Jun 25, 2015 at 4:12 PM leila salimi leilasal...@gmail.com wrote: Dear Mark, When I tried with new update of the state.cpt files, I got this error. Abort(1) on node 896 (rank 896 in comm 1140850688): Fatal error in MPI_Allreduce: Message truncated, error stack: MPI_Allreduce(912)...: MPI_Allreduce(sbuf=MPI_IN_PLACE, rbuf=0x7ffc783af760, count=4, MPI_DOUBLE, MPI_SUM, comm=0x8402) failed MPIR_Allreduce_impl(769).: MPIR_Allreduce_intra(419): MPIC_Sendrecv(467)...: MPIDI_Buffer_copy(73): Message truncated; 64 bytes received but buffer size is 32 Abort(1) on node 768 (rank 768 in comm 1140850688): Fatal error in MPI_Allreduce: Message truncated, error stack: MPI_Allreduce(912)...: MPI_Allreduce(sbuf=MPI_IN_PLACE, rbuf=0x7ffdba5176a0, count=4, MPI_DOUBLE, MPI_SUM, comm=0x8402) failed MPIR_Allreduce_impl(769).: MPIR_Allreduce_intra(419): MPIC_Sendrecv(467)...: MPIDI_Buffer_copy(73): Message truncated; 64 bytes received but buffer size is 32 ERROR: 0031-300 Forcing all remote tasks to exit due to exit code 1 in task 896 job.err.1011016.out 399L, 17608C Actually I don't know what is the problem! Regards, Leila On Thu, Jun 18, 2015 at 12:00 AM, leila salimi leilasal...@gmail.com wrote: I understand what you meant, I run only few steps for the other replicas and then continue with the whole replicas. I hope every thing is going well. Thanks
Re: [gmx-users] pretty large coulomb contribution to free energy
To test that patched GROMACS version there is not any information about how [ intermolecular-interactions ] must add to .top file in manual/your tutorials. Maybe you can paste here an example .top file you have recently used with that version :) Is that possible? 2015-06-27 1:56 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 6/26/15 4:44 PM, Ahmet Yıldırım wrote: Dear users, The free energy of decoupling the ligand from the complex I get is about 457 kcal/mol. If for ligand in solution I get -5 kcal/mol, and for the restraints -8 kcal/mol. Binding free energy is 457-5-8=444 kcal/mol. A value over 400-500 kcal/mol is not unexpected for decoupling the ligand from the complex? Anyone experienced similar problem? The problem is the intramolecular interaction of the ligand? How about this Gromacs version https://github.com/gromacs/gromacs/tree/022ad08b2fd0c1de085e88ac81a61841c4daea9c ? For proper absolute binding free energies, you need these restraints. I'm actually using that patched version now and it's essential for getting reasonable energies in protein-ligand complexes. Otherwise you sample a ton of totally nonphysical configurations in (nearly) decoupled states. Even just the pull code is not enough; that provides a translational restraint, but the orientation can vary. See, e.g. dx.doi.org/10.1021/ci300505n for a very robust method that can easily be done in GROMACS now using the intermolecular bondeds. -Justin Ligand I used is neutral. Gromacs version is 4.6.5 Free energy control parts of my input files are below. For decoupling the ligand from the complex # ; Free energy control stuff init-lambda-state= 5 free_energy = yes sc-alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 restraint-lambdas= 0.0 0.01 0.025 0.05 0.075 0.1 0.2 0.35 0.5 0.75 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 coul-lambdas = 0.0 0.00 0.000 0.00 0.000 0.0 0.0 0.00 0.0 0.00 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 vdw-lambdas = 0.0 0.00 0.000 0.00 0.000 0.0 0.0 0.00 0.0 0.00 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0 nstdhdl = 10 pull = umbrella pull_geometry = distance pull_dim = Y Y Y pull_start = no pull_init1 = 0.2980769 pull_ngroups = 1 pull_group0= atom-p pull_group1= atom-l pull_k1= 0.0 ; kJ*mol^(-1)*nm^(-2) pull_kB1 = 4184 ; kJ*mol^(-1)*nm^(-2) For solvation free energy ### ; Free energy control stuff init-lambda-state= 5 free_energy = yes sc-alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 coul-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 vdw-lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0 nstdhdl = 10 couple-intramol = yes couple-moltype = MOL couple-lambda0 = vdw-q couple-lambda1 = none -- == 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. -- Ahmet Yıldırım -- 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] 회신: Re: counting the number of water molecules surrounding proteins
Dear Justin
Thanks for your suggestion. I will try with g_select too.
Best,
Sang Eun Jee
div 원본 메시지 /divdiv발신: Justin Lemkul jalem...@vt.edu
/divdiv날짜:26/06/2015 19:56 (GMT-05:00) /divdiv수신:
gmx-us...@gromacs.org /divdiv제목: Re: [gmx-users] counting the number of
water molecules surrounding
proteins /divdiv
/div
On 6/26/15 4:50 PM, sang eun jee wrote:
Dear Gromacs Users
Hello.
I have a question about how to count the number of water molecules
surrounding protiens.
I have tried two methods and the results from two methods were different.
The first one is use g_trjorder -f structure.xtc -s structure.tpr -n
index.ndx -nshell water_in_0.22.xvg -r 0.22
I have chose first reference group as protein and second group water.
Using this method, I could calculate the number of water molecules in 0.22
nm as time from protein.
The second method is using mindist.
At first I have calcualted minimum distance from water to protien within
0.5 nm using g_mindist
g_mindist -s structure.tpr -f structure.xtc -n index.ndx -d 0.50
-respertime -od od.xvg -or mindrest.xvg
Here I chose the first reference group water and second reference group
protein. As long as I understand, mindrest.xvg include minimum distance
data of the water-protein per each water molecule.
And then using grep, I have extracted the number of water molecules in the
range of r0.22
grep -v '[#|@|S]' mindistres.xvg | awk '{a1=0;;for(i=2;i=NF;i++)
if($i'0.22') a1++;print $1,a1}' water_count.xvg
Then I could obtain the number of water molecules in 0.22 nm as a function
of time.
When I got time-averaged values of the number of water molecules within
0.22 nm, the value from first method is different from second method. I got
162 water molecules from first method, while I got 222 water molecules from
second one.
Does anyone have experience in this method?
I would just use gmx select to calculate the number of water oxygens within
some
distance of protein atoms of interest.
-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
==
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Re: [gmx-users] The pullf.xvg and pullx.xvg files
On 6/26/15 10:34 AM, Laura Tociu wrote: Dear Justin, I have done two parallel short pullings, one with pull_geometry = cylinder and one with pull_geometry = direction. When pull_geometry = direction, everything works perfectly: the grompp output says that the distance at start, as well as the reference at t=0 are both equal to 3.019 nm, and the pullx.xvg file reflects this: at t=0 the distance is also 3.019 nm. This distance is reasonable based on my geometry. The force at t=0 is 10^-6 and the COM pull energy in the md.log file is on the order of 10^-10. When pull_geometry = cylinder, the grompp output says the distance at start and the reference distance are 1.215 nm (which they aren't) but the distance at t=0 in the pullx.xvg file shows up as 2.8 nm (which it is roughly - it's hard to tell where the COM as computed by the cylinder approach would be but it is likely to be close to the COM as usually computed). This huge discrepancy leads to huge forces as well as energies at t=0. Is this some kind of bug that has been fixed since Gromacs 5.0.2, which is the version I'm using, or should I report it? I think since the distance Upgrading to 5.0.5 and trying again is the best way to answer that. I don't know whether or not this is a bug. computed by grompp and that in the pullx.xvg file at t=0 are different, the method will likely give inaccurate forces and thus PMF's... What do you think? Looking back over your setup again, I really don't think you need the cylinder geometry. That's really intended for layers in which the reference atoms will change over time, as in the example shown in the manual. Here, you have an ion and a protein; the reference atoms don't change, so some simpler geometry is more appropriate. -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] Energy minimisation goes to several values
On 6/26/15 11:54 AM, Kevin C Chan wrote: Thanks Justin for the reply. Honestly I thought minimizing a large and complex (usually biomolecular) system part by part instead of as a whole will effectively shorten the computational time cost while causing no effect on the final structure. When you say “impedes”, do you mean it causes a longer calculation time in total or it will give a bad final structure? Well, you're running three minimizations instead of one, and you're achieving an unstable result. I'd say the three-step approach is not worth doing :) Consider something really simple - a polar, surface residue on a protein surrounded by water. Let's say you freeze the protein and let the water relax. The local waters respond to the fixed geometry of the side chain, which is (maybe) from a crystal and therefore perhaps not the correct conformation in solution. So the waters reorganize a bit. Then you let the protein relax but the waters are fixed. The side chain responds to a fixed clathrate of water that have been minimized around the wrong side chain conformation. What have you achieved? Nothing. Sure, you then minimize the whole system, but your starting point is potentially less plausible than it was to start with! At minimum, it's just a waste of time. Occasional use of restraints can be beneficial in some cases. Any time you talk about absolutely fixing large groups of atoms (like immobilizing water), I think it's really a waste of time. If a single, unrestrained minimization still leads to an unstable system, then it's not your minimization protocol that's to blame, rather an unresolvable starting structure or a bad topology. -Justin Thanks in advance, Kevin On 26 Jun, 2015, at 22:21, gromacs.org_gmx-users-requ...@maillist.sys.kth.se mailto:gromacs.org_gmx-users-requ...@maillist.sys.kth.se gromacs.org_gmx-users-requ...@maillist.sys.kth.se mailto:gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: *From:*Justin Lemkul jalem...@vt.edu mailto:jalem...@vt.edu *Subject:**Re: [gmx-users] Energy minimisation goes to several values* *Date:*26 June, 2015 21:27:32 HKT *To:*gmx-us...@gromacs.org mailto:gmx-us...@gromacs.org *Reply-To:*gmx-us...@gromacs.org mailto:gmx-us...@gromacs.org On 6/25/15 9:45 PM, Kevin C Chan wrote: Dear Users, I am energy minimising a quite large solvated system containing protein and lipids (~800,000 atoms). I used to fix components of the system in order to speed-up energy minimisation and sometimes it is easier to debug such processes. Here is my protocol: 1. fix all except water and so to minimise water 2. fix water and then minimise all the rest atoms 3. fix nothin and then minimise the whole system While monitoring the energy of the system thought minimisations, it goes fine for step 1 and 2 and converged after just few hundred steps. However it goes back to several higher values of energy (bouncing between the values) and they started to increase very slowly for step 3. This makes no sense to me and did anyone have a similar experience? There are two unusual points: 1. The system energy drops suddenly instead of decreased gradually during step2 and then stays at a constant value. 2. If I use the resulting structure from step3 to proceed a, say, heating process, it simply blows up. To be clear, my system was solvated and auto-ionized using VMD tools and some water inside the membrane has been directly deleted. Backbone of the protein and phosphorus atoms of the membrane are under a position constraint during all the minimisations. I was choosing conjugate gradient for minimization. Does a normal minimization (just one overall minimization with nothing fixed) yield a stable starting point? Fixing atoms (using freezegrps?) often actually impedes minimization. -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 mailto:jalem...@outerbanks.umaryland.edu| (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- == 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
Re: [gmx-users] counting the number of water molecules surrounding proteins
On 6/26/15 4:50 PM, sang eun jee wrote:
Dear Gromacs Users
Hello.
I have a question about how to count the number of water molecules
surrounding protiens.
I have tried two methods and the results from two methods were different.
The first one is use g_trjorder -f structure.xtc -s structure.tpr -n
index.ndx -nshell water_in_0.22.xvg -r 0.22
I have chose first reference group as protein and second group water.
Using this method, I could calculate the number of water molecules in 0.22
nm as time from protein.
The second method is using mindist.
At first I have calcualted minimum distance from water to protien within
0.5 nm using g_mindist
g_mindist -s structure.tpr -f structure.xtc -n index.ndx -d 0.50
-respertime -od od.xvg -or mindrest.xvg
Here I chose the first reference group water and second reference group
protein. As long as I understand, mindrest.xvg include minimum distance
data of the water-protein per each water molecule.
And then using grep, I have extracted the number of water molecules in the
range of r0.22
grep -v '[#|@|S]' mindistres.xvg | awk '{a1=0;;for(i=2;i=NF;i++)
if($i'0.22') a1++;print $1,a1}' water_count.xvg
Then I could obtain the number of water molecules in 0.22 nm as a function
of time.
When I got time-averaged values of the number of water molecules within
0.22 nm, the value from first method is different from second method. I got
162 water molecules from first method, while I got 222 water molecules from
second one.
Does anyone have experience in this method?
I would just use gmx select to calculate the number of water oxygens within some
distance of protein atoms of interest.
-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!
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* For (un)subscribe requests visit
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Re: [gmx-users] energy minimization error
On 6/26/15 7:19 PM, James Lord wrote: Hi Justin, I have asked this before, but this time I started up from scratch and used the input files that I know they are fine but again I am getting this error, Would you please tell me what is wrong in my topology files and where about in .top files the bond length are defined? https://drive.google.com/file/d/0B0YMTXH1gmQsbkpjTU9tWGFkSDA/view?usp=sharing There's nothing I can do with a topology that's a series of #include statements. Please also remind me what this is all about so I don't have to go digging through the archives for something from a month ago. Lots of things have happened since then :) -Justin Cheers James On Mon, May 18, 2015 at 1:13 AM, Justin Lemkul jalem...@vt.edu wrote: On 5/16/15 11:35 PM, James Lord wrote: Hi Justin Thanks for this. Can you tell me which step(s) this bond length is defined What should I do (redo) to resolve this issue? The bonds are defined in the topology. The DD algorithm reads what's in the coordinate file and builds cells based on the geometry it finds there. Without a full description of what's in your system, what steps you've taken to prepare it (full commands, in order), there's little I can suggest because it would all be guesswork. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization error
Hi Justin, I have asked this before, but this time I started up from scratch and used the input files that I know they are fine but again I am getting this error, Would you please tell me what is wrong in my topology files and where about in .top files the bond length are defined? https://drive.google.com/file/d/0B0YMTXH1gmQsbkpjTU9tWGFkSDA/view?usp=sharing Cheers James On Mon, May 18, 2015 at 1:13 AM, Justin Lemkul jalem...@vt.edu wrote: On 5/16/15 11:35 PM, James Lord wrote: Hi Justin Thanks for this. Can you tell me which step(s) this bond length is defined What should I do (redo) to resolve this issue? The bonds are defined in the topology. The DD algorithm reads what's in the coordinate file and builds cells based on the geometry it finds there. Without a full description of what's in your system, what steps you've taken to prepare it (full commands, in order), there's little I can suggest because it would all be guesswork. -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.
Re: [gmx-users] Configuration bug preventing GROMACS 5.0 build with Intel compiler?
Just noticed this question from Sep 2014. The problem was that configuring with the Intel compiler and IntelMPI causes incorrect detection of _finite. This is caused by bugs in the IntelMPI wrappers for both gcc and intel compilers, including the MIC wrappers. I have patches available if someone want to have them. I have not had time to report this to Intel yet... -- Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden Internet: a...@hpc2n.umu.se Phone: +46 90 7866134 Fax: +46 90-580 14 Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se -- 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] error gcq#360
Dear gmx users, after running grompp -f em.mdp -c COM_ions.gro -p COM.top -o em.tpr I obtained: GROMACS: gmx grompp, VERSION 5.0 Executable: /software/local/el6/INTEL/gromacs/5.0.0/intel-ompi-fftw-blas-lapack/bin/gmx Library dir: /software/local/el6/INTEL/gromacs/5.0.0/intel-ompi-fftw-blas-lapack/share/gromacs/top Command line: grompp -f em.mdp -c COM_ions.gro -p COM.top -o em.tpr Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# Setting the LD random seed to 2993272762 Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'DNA' Excluding 3 bonded neighbours molecule type 'DNA2' Excluding 3 bonded neighbours molecule type 'Protein3' Excluding 3 bonded neighbours molecule type 'Protein4' Excluding 3 bonded neighbours molecule type 'Protein5' Excluding 3 bonded neighbours molecule type 'Protein6' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 1 bonded neighbours molecule type 'NA' Excluding 1 bonded neighbours molecule type 'CL' Removing all charge groups because cutoff-scheme=Verlet Analysing residue names: There are: 136DNA residues There are: 1140Protein residues There are: 557197 Water residues There are: 2152Ion residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 5090256.00 Calculating fourier grid dimensions for X Y Z Using a fourier grid of 216x216x216, spacing 0.119 0.119 0.119 Estimate for the relative computational load of the PME mesh part: 0.27 NOTE 1 [file em.mdp]: This run will generate roughly 586540 Mb of data There was 1 note gcq#360: error: too many template-parameter-lists (g++) At the end I have em.tpr file but I am not sure if everything is ok. Any suggestions. best regards Urszula - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- 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] error gcq#360
Hi, There's no problem - that's just a fun Gromacs Cool Quote (i.e. gcq), as the tools often print at the end of their run. This one is perhaps not a good wording! (There are ways to turn them off, if they annoy people.) Mark On Fri, Jun 26, 2015 at 3:24 PM Urszula Uciechowska urszula.uciechow...@biotech.ug.edu.pl wrote: Dear gmx users, after running grompp -f em.mdp -c COM_ions.gro -p COM.top -o em.tpr I obtained: GROMACS: gmx grompp, VERSION 5.0 Executable: /software/local/el6/INTEL/gromacs/5.0.0/intel-ompi-fftw-blas-lapack/bin/gmx Library dir: /software/local/el6/INTEL/gromacs/5.0.0/intel-ompi-fftw-blas-lapack/share/gromacs/top Command line: grompp -f em.mdp -c COM_ions.gro -p COM.top -o em.tpr Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# Setting the LD random seed to 2993272762 Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'DNA' Excluding 3 bonded neighbours molecule type 'DNA2' Excluding 3 bonded neighbours molecule type 'Protein3' Excluding 3 bonded neighbours molecule type 'Protein4' Excluding 3 bonded neighbours molecule type 'Protein5' Excluding 3 bonded neighbours molecule type 'Protein6' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 1 bonded neighbours molecule type 'NA' Excluding 1 bonded neighbours molecule type 'CL' Removing all charge groups because cutoff-scheme=Verlet Analysing residue names: There are: 136DNA residues There are: 1140Protein residues There are: 557197 Water residues There are: 2152Ion residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 5090256.00 Calculating fourier grid dimensions for X Y Z Using a fourier grid of 216x216x216, spacing 0.119 0.119 0.119 Estimate for the relative computational load of the PME mesh part: 0.27 NOTE 1 [file em.mdp]: This run will generate roughly 586540 Mb of data There was 1 note gcq#360: error: too many template-parameter-lists (g++) At the end I have em.tpr file but I am not sure if everything is ok. Any suggestions. best regards Urszula - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- 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] Energy minimisation goes to several values
On 6/25/15 9:45 PM, Kevin C Chan wrote: Dear Users, I am energy minimising a quite large solvated system containing protein and lipids (~800,000 atoms). I used to fix components of the system in order to speed-up energy minimisation and sometimes it is easier to debug such processes. Here is my protocol: 1. fix all except water and so to minimise water 2. fix water and then minimise all the rest atoms 3. fix nothin and then minimise the whole system While monitoring the energy of the system thought minimisations, it goes fine for step 1 and 2 and converged after just few hundred steps. However it goes back to several higher values of energy (bouncing between the values) and they started to increase very slowly for step 3. This makes no sense to me and did anyone have a similar experience? There are two unusual points: 1. The system energy drops suddenly instead of decreased gradually during step2 and then stays at a constant value. 2. If I use the resulting structure from step3 to proceed a, say, heating process, it simply blows up. To be clear, my system was solvated and auto-ionized using VMD tools and some water inside the membrane has been directly deleted. Backbone of the protein and phosphorus atoms of the membrane are under a position constraint during all the minimisations. I was choosing conjugate gradient for minimization. Does a normal minimization (just one overall minimization with nothing fixed) yield a stable starting point? Fixing atoms (using freezegrps?) often actually impedes minimization. -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.
