[gmx-users] Checksum wrong
Dear users, When I restart one of lambda points for free energy calculation, Gromacs gives the following error. Whereas the md_0.xvg file exists in the folder. I hope the md_0.xvg can append? Command: mdrun -v -s md_0.tpr -cpi md_0.cpt -cpo md_0-1.cpt -dhdl md_0.xvg -x md_0.xtc -e md_0.edr -g md_0.log -append Fatal error: Checksum wrong for 'md_0.xvg'. The file has been replaced or its contents have been modified. Cannot do appending because of this condition. -- 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.
Re: [gmx-users] Making disulfide bonds between protein and glutathion (GSH)
Many thanks Justin :) Tuong Vy 2015-05-28 21:01 GMT+09:00 Justin Lemkul jalem...@vt.edu: On 5/27/15 10:23 PM, Vy Phan wrote: Dear Gromas User, I want to making disulfide bonds between protein and glutathion (GSH). The topology for GSH I got from Produg serve. Don't do this; the topology will be of very poor quality. See http://pubs.acs.org/doi/abs/10.1021/ci100335w Could you please show me how I can make the disulfide bons between protein and GSH? Add an entry in specbond.dat http://www.gromacs.org/Documentation/File_Formats/specbond.dat -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] Cyclohexane simulation problem
Dear All, I am interested in simulation of cyclohexane box based on Lemkul tutorial. At first I built a box using following commandgmx insert-molecules -ci chx.gro -nmol 500 -box 2.154434 2.154434 2.154434 -o chx_box.gro (I want a box with 10 nm3 volume)after run several times and convergence I have a box with 88 CHX. then I minimized energy using following mdp file:; minim.mdp - used as input into grompp to generate em.tpr integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 100.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 50 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1 ; Short-range electrostatic cut-off rvdw = 1 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no)== OOPS!! I got following fatal error = GROMACS: gmx grompp, VERSION 5.0.4 Executable: /usr/local/gromacs/bin/gmx Library dir: /usr/local/gromacs/share/gromacs/top Command line: gmx grompp -f minim.mdp -c chx_box.gro -p chx_box.top -o em.tpr Back Off! I just backed up mdout.mdp to ./#mdout.mdp.41# NOTE 1 [file minim.mdp]: With Verlet lists the optimal nstlist is = 10, with GPUs = 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Setting the LD random seed to 1763529642 Generated 165 of the 1596 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'chx' Warning: atom name 1 in chx_box.top and chx_box.gro does not match (CAA - AA) Warning: atom name 2 in chx_box.top and chx_box.gro does not match (CAB - AB) Warning: atom name 3 in chx_box.top and chx_box.gro does not match (CAE - AE) Warning: atom name 4 in chx_box.top and chx_box.gro does not match (CAF - AF) Warning: atom name 5 in chx_box.top and chx_box.gro does not match (CAD - AD) Warning: atom name 6 in chx_box.top and chx_box.gro does not match (CAC - AC) Warning: atom name 7 in chx_box.top and chx_box.gro does not match (CAA - AA) Warning: atom name 8 in chx_box.top and chx_box.gro does not match (CAB - AB) Warning: atom name 9 in chx_box.top and chx_box.gro does not match (CAE - AE) Warning: atom name 10 in chx_box.top and chx_box.gro does not match (CAF - AF) Warning: atom name 11 in chx_box.top and chx_box.gro does not match (CAD - AD) Warning: atom name 12 in chx_box.top and chx_box.gro does not match (CAC - AC) Warning: atom name 13 in chx_box.top and chx_box.gro does not match (CAA - AA) Warning: atom name 14 in chx_box.top and chx_box.gro does not match (CAB - AB) Warning: atom name 15 in chx_box.top and chx_box.gro does not match (CAE - AE) Warning: atom name 16 in chx_box.top and chx_box.gro does not match (CAF - AF) Warning: atom name 17 in chx_box.top and chx_box.gro does not match (CAD - AD) Warning: atom name 18 in chx_box.top and chx_box.gro does not match (CAC - AC) Warning: atom name 19 in chx_box.top and chx_box.gro does not match (CAA - AA) Warning: atom name 20 in chx_box.top and chx_box.gro does not match (CAB - AB) (more than 20 non-matching atom names) WARNING 1 [file chx_box.top, line 58]: 528 non-matching atom names atom names from chx_box.top will be used atom names from chx_box.gro will be ignored Removing all charge groups because cutoff-scheme=Verlet Analysing residue names: There are: 88 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 1581.00 WARNING 2 [file minim.mdp]: You are using full electrostatics treatment PME for a system without charges. This costs a lot of performance for just processing zeros, consider using Cut-off instead. Calculating fourier grid dimensions for X Y Z Using a fourier grid of 20x20x20, spacing 0.108 0.108 0.108 Estimate for the relative computational load of the PME mesh part: 0.23 This run will generate roughly 2 Mb of data There was 1 note There were 2 warnings --- Program gmx, VERSION 5.0.4 Source code file: /home/mohsen/Downloads/gromacs-5.0.4/src/gromacs/gmxpreprocess/grompp.c, line: 2087 Fatal error: Too many warnings (2), gmx terminated. If you are sure all warnings are harmless, use the -maxwarn option. For more information and tips for troubleshooting, please check the GROMACS website at
Re: [gmx-users] Water organic solvents mixtures: Which force field to use and best practice to derive parameters
Hi Not because I developed ACPYPE, but if I’d like to be the most rigorous as possible, I’d go with ACPYPE and RED (http://q4md-forcefieldtools.org/). Alan On 29 May 2015 at 20:53, Ebert Maximilian m.eb...@umontreal.ca wrote: I continued to define good partial charges using the tools suggested. I found that the combination of Maestro + ffconv or mktop, ACPYPE and antechamber + mktop have all advantages and disadvantages depending on the organic molecule. for instance for acetone with maestro and mktop i could achieve the same topology as virtual chemistry. I next tried to generate a topology for iso-propanol. Here ACPYPE charges with the mktop atom types gave the closes density to the experimental one. I also tried to calculate the heat capacity with Cp and Cv to compare it with the literature. My box is 2.3x2.3x2.3nm large and has about 150 molecules of the organic solvent. After 1ns of NPT i get values which are 5x higher than the literature value (gmx energy -f npt.edr -fluct_props -nmol 100). I also tried a box 5x5x5nm with over 1000 molecules and got the same result. Any idea why the simulation using OPLS AA FF is so far of when it comes to the heat capacity? thanks max On May 28, 2015, at 9:19 AM, Ebert Maximilian m.eb...@umontreal.ca wrote: Thanks Justin and Kalev this brings me already much further. I tried ffld_server and it works just fine. However, it is like a black box. I can’t really find the documentation on how ffld_server gets the charges. Do you know where to find the documentation? Thanks On May 28, 2015, at 2:22 AM, Kalev Takkis kalev.tak...@gmail.com wrote: If you're after OPLS topologies for GROMACS then one way to derive them is via Schrödinger's Maestro (free academics version is sufficient) and Andrey Frolov's ffconv script (http://frolov-pchem.wikispaces.com/ffconv.py). You can create a force field represesentation of a molecule with the former (described here http://www.schrodinger.com/kb/809) and then convert it to GROMACS format with the latter. All the best, Kalev On 28 May 2015 at 03:37, Mohd Farid Ismail mohd.farid.ism...@yandex.com wrote: You can try R.E.D. Server. It has more charge models (I don't know whether that will help). Also, IMO, one should target the density and the static dielectric constant when it comes to VDW and partial charges. I saw a recent paper that might be of interest to you http://pubs.acs.org/doi/abs/10.1021/jp3002383 -- Mohd Farid Ismail 28.05.2015, 05:13, Ebert Maximilian m.eb...@umontreal.ca: I just finished a 1 ns NPT calculation of a 2.3x2.3x2.3 nm box filled with acetone (130 molecules). The expected density at 300K is 784.1 kg/m^3. For the virtual chemistry parameters i calculated 798.6 (close to the 800.1±0.2 value on their website) and for the parameter derived as explain in previous mail I got 817.0 which seems too high. Does anybody has an advice how I could improve the derivation of my parameters? Thank you very much, max On May 27, 2015, at 3:25 PM, Ebert Maximilian m.eb...@umontreal.ca wrote: I read more about organic solvents in MD and came to the conclusion that OPLS is indeed the best way to go. Since I couldn’t really find an accessible tutorial how to derive topology files for GROMACS and the FF OPLS/AA I will document my progress here. Maybe this is of help for somebody in the future. In addition, I would like to ask the community to help me in case you see problems with my approach. Once I have a good protocol I will write a tutorial and make it available online. To validate my approach I am trying to create a parameter set for acetone which I found on http://virtualchemistry.org. To generate the OPLS topology I used a tool suggested by many people called mktop in version 2.2.1. I downloaded the ideal geometry of acetone from Ligand Expo and generated a GROMACS topology file using the following command: mktop_2.2.1.pl -i ACN_ideal.pdb -o acn_topology.top -ff opls -conect yes In order to get the charges for this organic molecule I downloaded the most recent amber tools and compiled it. I used the AM1-BCC charge model to generate charges for acetone using the following instructions in antechamber: antechamber -i ACN_ideal.pdb -fi pdb -o acn.mol2 -fo mol2 -c bcc -s 2 I opened the resulting mol2 file in Chimera to map the atoms to the atoms in my .top file. The charges calculated by antechamber look reasonable and are comparable to the validated OPLS topology from virtual chemistry: virtual chemistry charges [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_280 1 LIG C 1 0.47 12.011 2 opls_135 1 LIG C 2 -0.18 12.011 3 opls_135 1 LIG
[gmx-users] regarding pdb2gmx
Hi all,
I have a general query about the basic functioning of pdb2gmx. I
recently observed that when I take a PDB file for a DNA molecule and build
its topology via pdb2gmx (in CHARMM27 ff) it automatically builds it
without any hitches. If I look at the .itp file made for the DNA chain it
looks like,
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
; residue 1 DC rtp DC q -0.5
1ON5 1 DCO5' 1 -0.6615.9994 ;
qtot -0.66
2HN5 1 DCH5T 2 0.43 1.008 ;
qtot -0.23
3 CN8B 1 DCC5' 3 0.05 12.011 ;
qtot -0.18
4HN8 1 DC H5'1 4 0.09 1.008 ;
qtot -0.09
5HN8 1 DC H5'2 5 0.09 1.008 ;
qtot 0
6CN7 1 DCC4' 6 0.16 12.011 ;
qtot 0.16
7HN7 1 DCH4' 7 0.09 1.008 ;
qtot 0.25
8ON6 1 DCO4' 8 -0.515.9994 ;
qtot -0.25
9 CN7B 1 DCC1' 9 0.16 12.011 ;
qtot -0.09
10HN7 1 DCH1' 10 0.09 1.008 ;
qtot 0
11NN2 1 DC N1 11 -0.13 14.007 ;
qtot -0.13
12CN3 1 DC C6 12 0.05 12.011 ;
qtot -0.08
13HN3 1 DC H6 13 0.17 1.008 ;
qtot 0.09
14CN3 1 DC C5 14 -0.13 12.011 ;
qtot -0.04
15HN3 1 DC H5 15 0.07 1.008 ;
qtot 0.03
16CN1 1 DC C2 16 0.52 12.011 ;
qtot 0.55
17 ON1C 1 DC O2 17 -0.4915.9994 ;
qtot 0.06
18NN3 1 DC N3 18 -0.66 14.007 ;
qtot -0.6
19CN2 1 DC C4 19 0.65 12.011 ;
qtot 0.05
20NN1 1 DC N4 20 -0.75 14.007 ;
qtot -0.7
21HN1 1 DCH41 21 0.37 1.008 ;
qtot -0.33
22HN1 1 DCH42 22 0.33 1.008 ;
qtot 0
23CN8 1 DCC2' 23 -0.18 12.011 ;
qtot -0.18
24HN8 1 DC H2'1 24 0.09 1.008 ;
qtot -0.09
25HN8 1 DC H2'2 25 0.09 1.008 ;
qtot 0
26CN7 1 DCC3' 26 0.01 12.011 ;
qtot 0.01
27HN7 1 DCH3' 27 0.09 1.008 ;
qtot 0.1
28ON2 1 DCO3' 28 -0.5715.9994 ;
qtot -0.47
For one residue.
However, if you look at the [ bond ] section of this .itp file it looks
like,
[ bonds ]
; aiaj functc0c1c2c3
1 2 1
1 3 1
3 4 1
3 5 1
3 6 1
6 7 1
6 8 1
626 1
8 9 1
910 1
911 1
923 1
1112 1
1116 1
1213 1
There are no parameters in the right and by principle grompp should
complain about this. But the simulation runs fine and the proper
interactions with the desired outcomes are always obtained. However, things
get altered when I proceed to model anything else than a DNA/protein. As
for example, I have made a topology for tetramethyl ammonium ion ( in
CHARMM 27) and as usual it lacks these parameters in all the [ bonds ],
{angle ] or [ dihedral ] sections. I changed the .top extension to tma.itp
and included in the system topology for a double stranded DNA molecule
according to standard protocols. Now when I start grompp it screams about
the 'missing parameters in the tma.itp ffile'. My question is everytime I
model something my CHARMM, do I have to include parameters such as force
constant, phi0, b0, mult etc from the ffbonded.itp file manually or does
pdb2gmx should write it looking at the connectivity mentioned in the PDB
file? The same thing goes for writing sigma and epsilon terms from the
ffnonbonde.itp file manually or pdb2gmx should do it by default? I have
another question that is it ok not to specify the [ atomtypes ] and [
pairtypes ] in the .itp file because without these being specified
properly, is it possible that the correct non bonding interaction arises? I
have always seen SWISSPARAM and ATB topologies come with all these things
mentioned from the scratch but with pdb2gmx I have never seen it. So, is it
like pdb2gmx gives only the atoms making the bonds, angles, prop and
improp. dihedrals (atomtypes already mentioned in the aminoacids.rtp file)
and the rest of the parameters are to placed manually or am i missing
something regarding pdb2gmx( some flags)??
Recently, I wanted to simulate graphene and although the ideal job is to go
with g_x2top, issuing
Re: [gmx-users] regarding pdb2gmx
On 5/30/15 6:40 AM, soumadwip ghosh wrote:
Hi all,
I have a general query about the basic functioning of pdb2gmx. I
recently observed that when I take a PDB file for a DNA molecule and build
its topology via pdb2gmx (in CHARMM27 ff) it automatically builds it
without any hitches. If I look at the .itp file made for the DNA chain it
looks like,
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
; residue 1 DC rtp DC q -0.5
1ON5 1 DCO5' 1 -0.6615.9994 ;
qtot -0.66
2HN5 1 DCH5T 2 0.43 1.008 ;
qtot -0.23
3 CN8B 1 DCC5' 3 0.05 12.011 ;
qtot -0.18
4HN8 1 DC H5'1 4 0.09 1.008 ;
qtot -0.09
5HN8 1 DC H5'2 5 0.09 1.008 ;
qtot 0
6CN7 1 DCC4' 6 0.16 12.011 ;
qtot 0.16
7HN7 1 DCH4' 7 0.09 1.008 ;
qtot 0.25
8ON6 1 DCO4' 8 -0.515.9994 ;
qtot -0.25
9 CN7B 1 DCC1' 9 0.16 12.011 ;
qtot -0.09
10HN7 1 DCH1' 10 0.09 1.008 ;
qtot 0
11NN2 1 DC N1 11 -0.13 14.007 ;
qtot -0.13
12CN3 1 DC C6 12 0.05 12.011 ;
qtot -0.08
13HN3 1 DC H6 13 0.17 1.008 ;
qtot 0.09
14CN3 1 DC C5 14 -0.13 12.011 ;
qtot -0.04
15HN3 1 DC H5 15 0.07 1.008 ;
qtot 0.03
16CN1 1 DC C2 16 0.52 12.011 ;
qtot 0.55
17 ON1C 1 DC O2 17 -0.4915.9994 ;
qtot 0.06
18NN3 1 DC N3 18 -0.66 14.007 ;
qtot -0.6
19CN2 1 DC C4 19 0.65 12.011 ;
qtot 0.05
20NN1 1 DC N4 20 -0.75 14.007 ;
qtot -0.7
21HN1 1 DCH41 21 0.37 1.008 ;
qtot -0.33
22HN1 1 DCH42 22 0.33 1.008 ;
qtot 0
23CN8 1 DCC2' 23 -0.18 12.011 ;
qtot -0.18
24HN8 1 DC H2'1 24 0.09 1.008 ;
qtot -0.09
25HN8 1 DC H2'2 25 0.09 1.008 ;
qtot 0
26CN7 1 DCC3' 26 0.01 12.011 ;
qtot 0.01
27HN7 1 DCH3' 27 0.09 1.008 ;
qtot 0.1
28ON2 1 DCO3' 28 -0.5715.9994 ;
qtot -0.47
For one residue.
However, if you look at the [ bond ] section of this .itp file it looks
like,
[ bonds ]
; aiaj functc0c1c2c3
1 2 1
1 3 1
3 4 1
3 5 1
3 6 1
6 7 1
6 8 1
626 1
8 9 1
910 1
911 1
923 1
1112 1
1116 1
1213 1
There are no parameters in the right and by principle grompp should
complain about this. But the simulation runs fine and the proper
interactions with the desired outcomes are always obtained. However, things
get altered when I proceed to model anything else than a DNA/protein. As
for example, I have made a topology for tetramethyl ammonium ion ( in
CHARMM 27) and as usual it lacks these parameters in all the [ bonds ],
{angle ] or [ dihedral ] sections. I changed the .top extension to tma.itp
and included in the system topology for a double stranded DNA molecule
according to standard protocols. Now when I start grompp it screams about
the 'missing parameters in the tma.itp ffile'. My question is everytime I
model something my CHARMM, do I have to include parameters such as force
constant, phi0, b0, mult etc from the ffbonded.itp file manually or does
pdb2gmx should write it looking at the connectivity mentioned in the PDB
file? The same thing goes for writing sigma and epsilon terms from the
ffnonbonde.itp file manually or pdb2gmx should do it by default? I have
another question that is it ok not to specify the [ atomtypes ] and [
pairtypes ] in the .itp file because without these being specified
properly, is it possible that the correct non bonding interaction arises? I
have always seen SWISSPARAM and ATB topologies come with all these things
mentioned from the scratch but with pdb2gmx I have never seen it. So, is it
like pdb2gmx gives only the atoms making the bonds, angles, prop and
improp. dihedrals (atomtypes already mentioned in the aminoacids.rtp file)
and the rest of the parameters are to placed manually or am i missing
something regarding pdb2gmx( some flags)??
Re: [gmx-users] Cyclohexane simulation problem
On 5/30/15 3:44 AM, mohsen shahlaei wrote: Dear All, I am interested in simulation of cyclohexane box based on Lemkul tutorial. At first I built a box using following commandgmx insert-molecules -ci chx.gro -nmol 500 -box 2.154434 2.154434 2.154434 -o chx_box.gro (I want a box with 10 nm3 volume)after run several times and convergence I have a box with 88 CHX. then I minimized energy using following mdp file:; minim.mdp - used as input into grompp to generate em.tpr integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 100.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 50 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 1; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type= grid; Method to determine neighbor list (simple, grid) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1; Short-range electrostatic cut-off rvdw= 1; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions (yes/no)== OOPS!! I got following fatal error = GROMACS: gmx grompp, VERSION 5.0.4 Executable: /usr/local/gromacs/bin/gmx Library dir: /usr/local/gromacs/share/gromacs/top Command line: gmx grompp -f minim.mdp -c chx_box.gro -p chx_box.top -o em.tpr Back Off! I just backed up mdout.mdp to ./#mdout.mdp.41# NOTE 1 [file minim.mdp]: With Verlet lists the optimal nstlist is = 10, with GPUs = 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Setting the LD random seed to 1763529642 Generated 165 of the 1596 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'chx' Warning: atom name 1 in chx_box.top and chx_box.gro does not match (CAA - AA) Warning: atom name 2 in chx_box.top and chx_box.gro does not match (CAB - AB) Warning: atom name 3 in chx_box.top and chx_box.gro does not match (CAE - AE) Warning: atom name 4 in chx_box.top and chx_box.gro does not match (CAF - AF) Warning: atom name 5 in chx_box.top and chx_box.gro does not match (CAD - AD) Warning: atom name 6 in chx_box.top and chx_box.gro does not match (CAC - AC) Warning: atom name 7 in chx_box.top and chx_box.gro does not match (CAA - AA) Warning: atom name 8 in chx_box.top and chx_box.gro does not match (CAB - AB) Warning: atom name 9 in chx_box.top and chx_box.gro does not match (CAE - AE) Warning: atom name 10 in chx_box.top and chx_box.gro does not match (CAF - AF) Warning: atom name 11 in chx_box.top and chx_box.gro does not match (CAD - AD) Warning: atom name 12 in chx_box.top and chx_box.gro does not match (CAC - AC) Warning: atom name 13 in chx_box.top and chx_box.gro does not match (CAA - AA) Warning: atom name 14 in chx_box.top and chx_box.gro does not match (CAB - AB) Warning: atom name 15 in chx_box.top and chx_box.gro does not match (CAE - AE) Warning: atom name 16 in chx_box.top and chx_box.gro does not match (CAF - AF) Warning: atom name 17 in chx_box.top and chx_box.gro does not match (CAD - AD) Warning: atom name 18 in chx_box.top and chx_box.gro does not match (CAC - AC) Warning: atom name 19 in chx_box.top and chx_box.gro does not match (CAA - AA) Warning: atom name 20 in chx_box.top and chx_box.gro does not match (CAB - AB) (more than 20 non-matching atom names) This suggests bad formatting of your input. You've got a column shifted somewhere. Make sure that isn't impacting the interpretation of the coordinates, which could be nonsense if they are similarly affected. WARNING 1 [file chx_box.top, line 58]: 528 non-matching atom names atom names from chx_box.top will be used atom names from chx_box.gro will be ignored Removing all charge groups because cutoff-scheme=Verlet Analysing residue names: There are:88 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 1581.00 WARNING 2 [file minim.mdp]: You are using full electrostatics treatment PME for a system without charges. This costs a lot of performance for just processing zeros, consider using Cut-off instead. grompp is trying to help you out. Change the coulombtype setting accordingly. You have no charges in a UA cyclohexane model, so the electrostatics method is totally irrelevant. -Justin Calculating fourier grid dimensions for X Y Z Using a fourier grid of 20x20x20, spacing 0.108 0.108 0.108 Estimate for the relative computational load of the PME mesh part: 0.23 This run will generate roughly 2 Mb of
Re: [gmx-users] Should I fix my drugs during membrane penetration simulation?
On 5/30/15 1:25 AM, yoochan wrote: Dear all, I’m trying to do umbrella sampling simulation which drugs penetrate the POPC membrane. I have trouble what if I do npt or umbrella simulation, the drugs move around from the initial location. (I got each 0.1 nm spacing window for npt and umbrella simulation) Well, the drug should always move, but it should be restrained according to what settings you're using. So, these results cannot have suitable G_WHAM analysis because of lack of results files at the certain coordinates. Should I have to fix the drugs to keep and satisfy G_WHAM analysis? Here I linked my simulation results and mdp files. 1.) npt_and_umbrella Simulation results. https://www.dropbox.com/s/w2gq3y686kmw3uc/npt_vs_umbrella_1.png?dl=0 https://www.dropbox.com/s/w2gq3y686kmw3uc/npt_vs_umbrella_1.png?dl=0 2) npt.mdp https://www.dropbox.com/s/y1tg4fhxk6mcpul/npt.mdp?dl=0 https://www.dropbox.com/s/y1tg4fhxk6mcpul/npt.mdp?dl=0 3) umbrella.mdp https://www.dropbox.com/s/0n8bp5rlu6olz3i/umbrella.mdp?dl=0 https://www.dropbox.com/s/0n8bp5rlu6olz3i/umbrella.mdp?dl=0 You're using a restraint in z, which means the drug can move freely in x and y; this is probably what you're referring to above. The better method for this is probably the cylinder geometry, which is designed for purposes like these. See the manual. -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] Cyclohexane simulation problem
Please keep the discussion on the mailing list. On 5/30/15 8:44 AM, mohsen shahlaei wrote: Dear Justin, Thanks, could you please explain what is difference between Cut-off and PME in calculation of electrostatic interactions Simply, a cutoff is what it says it is - a plain truncation at a finite distance. For electrostatics, this is very crude and shouldn't be used in modern simulations. For your system, which has no charges, it doesn't matter. PME takes long-range interactions into account. The full description of PME and why people generally use it is way beyond what I'm will to type out, so suffice it to say you should be reading the description of the algorithm in the manual and the citations provided therein. -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] regarding pdb2gmx
Thanks Justin for your insights. So when I am making the topology of DNA via ppdb2gmx using CHARMM, the parameters in the .itp files are not adequate and I should place them manually everytime I make a molecule topology with pdb2gmx? In some of my previous works actually the DNA molecule gave outcomes which were pretty much expected. So, just like I have put all the missing parameters in the .cnt.itp file should I do the same with the dna.itp generated by pdb2gmx in order to ensure correct interactions? thanks for your time in advance Soumadwip Research Fellow IITB India -- 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] regarding pdb2gmx
On 5/30/15 10:24 AM, soumadwip ghosh wrote: Thanks Justin for your insights. So when I am making the topology of DNA via ppdb2gmx using CHARMM, the parameters in the .itp files are not adequate and I should place them manually everytime I make a molecule topology with pdb2gmx? In some of my previous works actually the DNA molecule gave outcomes which were pretty much expected. So, just like I have put all the missing parameters in the .cnt.itp file should I do the same with the dna.itp generated by pdb2gmx in order to ensure correct interactions? No. The parameters for DNA exist in the force field, so grompp looks them up, finds them, and carries on happily. Again, this is how all the force fields work except GROMOS. -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.
